diff --git a/Cargo.lock b/Cargo.lock
index 2c31279a40..dd59fde101 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1453,6 +1453,7 @@ dependencies = [
  "dynasmrt",
  "libffi",
  "libffi-sys",
+ "log",
  "serde",
  "serde-value",
  "serde_json",
@@ -1557,6 +1558,7 @@ dependencies = [
  "deno_core",
  "filetime",
  "fs3",
+ "log",
  "once_cell",
  "os_pipe",
  "rand",
diff --git a/bench_util/profiling.rs b/bench_util/profiling.rs
index 2393649886..151a29e599 100644
--- a/bench_util/profiling.rs
+++ b/bench_util/profiling.rs
@@ -39,6 +39,7 @@ macro_rules! bench_or_profile {
   };
 }
 
+#[allow(clippy::print_stdout)]
 pub fn run_profiles(opts: &TestOpts, tests: Vec<TestDescAndFn>) {
   let tests = filter_tests(opts, tests);
   // let decs = tests.iter().map(|t| t.desc.clone()).collect();
diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index 0ef02be392..dca9cfa492 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -3889,6 +3889,7 @@ fn eval_parse(flags: &mut Flags, matches: &mut ArgMatches) {
   // TODO(@satyarohith): remove this flag in 2.0.
   let as_typescript = matches.get_flag("ts");
 
+  #[allow(clippy::print_stderr)]
   if as_typescript {
     eprintln!(
       "⚠️ {}",
@@ -4218,6 +4219,8 @@ fn test_parse(flags: &mut Flags, matches: &mut ArgMatches) {
   let no_run = matches.get_flag("no-run");
   let trace_leaks =
     matches.get_flag("trace-ops") || matches.get_flag("trace-leaks");
+
+  #[allow(clippy::print_stderr)]
   if trace_leaks && matches.get_flag("trace-ops") {
     // We can't change this to use the log crate because its not configured
     // yet at this point since the flags haven't been parsed. This flag is
@@ -4267,10 +4270,17 @@ fn test_parse(flags: &mut Flags, matches: &mut ArgMatches) {
     // yet at this point since the flags haven't been parsed. This flag is
     // deprecated though so it's not worth changing the code to use the log
     // crate here and this is only done for testing anyway.
-    eprintln!(
-      "⚠️ {}",
-      crate::colors::yellow("The `--jobs` flag is deprecated and will be removed in Deno 2.0.\nUse the `--parallel` flag with possibly the `DENO_JOBS` environment variable instead.\nLearn more at: https://docs.deno.com/runtime/manual/basics/env_variables"),
-    );
+    #[allow(clippy::print_stderr)]
+    {
+      eprintln!(
+        "⚠️ {}",
+        crate::colors::yellow(concat!(
+          "The `--jobs` flag is deprecated and will be removed in Deno 2.0.\n",
+          "Use the `--parallel` flag with possibly the `DENO_JOBS` environment variable instead.\n",
+          "Learn more at: https://docs.deno.com/runtime/manual/basics/env_variables"
+        )),
+      );
+    }
     if let Some(value) = matches.remove_one::<NonZeroUsize>("jobs") {
       Some(value)
     } else {
diff --git a/cli/args/mod.rs b/cli/args/mod.rs
index 3b5d79ef3c..bca7cc0f66 100644
--- a/cli/args/mod.rs
+++ b/cli/args/mod.rs
@@ -747,9 +747,12 @@ impl CliOptions {
         format!("for: {}", insecure_allowlist.join(", "))
       };
       let msg =
-        format!("DANGER: TLS certificate validation is disabled {domains}");
-      // use eprintln instead of log::warn so this always gets shown
-      eprintln!("{}", colors::yellow(msg));
+        format!("DANGER: TLS certificate validation is disabled {}", domains);
+      #[allow(clippy::print_stderr)]
+      {
+        // use eprintln instead of log::warn so this always gets shown
+        eprintln!("{}", colors::yellow(msg));
+      }
     }
 
     let maybe_lockfile = maybe_lockfile.filter(|_| !force_global_cache);
diff --git a/cli/bench/main.rs b/cli/bench/main.rs
index 9bae6fab60..8f0627558b 100644
--- a/cli/bench/main.rs
+++ b/cli/bench/main.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 use deno_core::error::AnyError;
 use deno_core::serde_json;
 use deno_core::serde_json::Value;
diff --git a/cli/file_fetcher.rs b/cli/file_fetcher.rs
index 01e1e31583..eda579b2b4 100644
--- a/cli/file_fetcher.rs
+++ b/cli/file_fetcher.rs
@@ -739,6 +739,8 @@ async fn fetch_no_follow<'a>(
   Ok(FetchOnceResult::Code(body, result_headers))
 }
 
+#[allow(clippy::print_stdout)]
+#[allow(clippy::print_stderr)]
 #[cfg(test)]
 mod tests {
   use crate::cache::GlobalHttpCache;
diff --git a/cli/main.rs b/cli/main.rs
index 3b103e7807..4f866ee21b 100644
--- a/cli/main.rs
+++ b/cli/main.rs
@@ -235,6 +235,7 @@ async fn run_subcommand(flags: Flags) -> Result<i32, AnyError> {
   handle.await?
 }
 
+#[allow(clippy::print_stderr)]
 fn setup_panic_hook() {
   // This function does two things inside of the panic hook:
   // - Tokio does not exit the process when a task panics, so we define a custom
@@ -259,6 +260,7 @@ fn setup_panic_hook() {
   }));
 }
 
+#[allow(clippy::print_stderr)]
 fn exit_with_message(message: &str, code: i32) -> ! {
   eprintln!(
     "{}: {}",
@@ -289,6 +291,7 @@ fn exit_for_error(error: AnyError) -> ! {
   exit_with_message(&error_string, error_code);
 }
 
+#[allow(clippy::print_stderr)]
 pub(crate) fn unstable_exit_cb(feature: &str, api_name: &str) {
   eprintln!(
     "Unstable API '{api_name}'. The `--unstable-{}` flag must be provided.",
@@ -298,6 +301,7 @@ pub(crate) fn unstable_exit_cb(feature: &str, api_name: &str) {
 }
 
 // TODO(bartlomieju): remove when `--unstable` flag is removed.
+#[allow(clippy::print_stderr)]
 pub(crate) fn unstable_warn_cb(feature: &str, api_name: &str) {
   eprintln!(
     "⚠️  {}",
@@ -369,7 +373,9 @@ fn resolve_flags_and_init(
 
   // TODO(bartlomieju): remove when `--unstable` flag is removed.
   if flags.unstable_config.legacy_flag_enabled {
+    #[allow(clippy::print_stderr)]
     if matches!(flags.subcommand, DenoSubcommand::Check(_)) {
+      // can't use log crate because that's not setup yet
       eprintln!(
         "⚠️  {}",
         colors::yellow(
diff --git a/cli/mainrt.rs b/cli/mainrt.rs
index 59efa026c5..6a363c04b5 100644
--- a/cli/mainrt.rs
+++ b/cli/mainrt.rs
@@ -36,6 +36,7 @@ use std::env::current_exe;
 
 use crate::args::Flags;
 
+#[allow(clippy::print_stderr)]
 pub(crate) fn unstable_exit_cb(feature: &str, api_name: &str) {
   eprintln!(
     "Unstable API '{api_name}'. The `--unstable-{}` flag must be provided.",
@@ -44,6 +45,7 @@ pub(crate) fn unstable_exit_cb(feature: &str, api_name: &str) {
   std::process::exit(70);
 }
 
+#[allow(clippy::print_stderr)]
 fn exit_with_message(message: &str, code: i32) -> ! {
   eprintln!(
     "{}: {}",
@@ -57,7 +59,7 @@ fn unwrap_or_exit<T>(result: Result<T, AnyError>) -> T {
   match result {
     Ok(value) => value,
     Err(error) => {
-      let mut error_string = format!("{error:?}");
+      let mut error_string = format!("{:?}", error);
 
       if let Some(e) = error.downcast_ref::<JsError>() {
         error_string = format_js_error(e);
diff --git a/cli/ops/jupyter.rs b/cli/ops/jupyter.rs
index e7e206de58..1c60bc2bc3 100644
--- a/cli/ops/jupyter.rs
+++ b/cli/ops/jupyter.rs
@@ -76,13 +76,13 @@ pub fn op_print(
 
   if is_err {
     if let Err(err) = sender.send(StdioMsg::Stderr(msg.into())) {
-      eprintln!("Failed to send stderr message: {}", err);
+      log::error!("Failed to send stderr message: {}", err);
     }
     return Ok(());
   }
 
   if let Err(err) = sender.send(StdioMsg::Stdout(msg.into())) {
-    eprintln!("Failed to send stdout message: {}", err);
+    log::error!("Failed to send stdout message: {}", err);
   }
   Ok(())
 }
diff --git a/cli/tools/bench/reporters.rs b/cli/tools/bench/reporters.rs
index 9cc035f8f1..b5229cf0ad 100644
--- a/cli/tools/bench/reporters.rs
+++ b/cli/tools/bench/reporters.rs
@@ -50,6 +50,7 @@ impl JsonReporter {
   }
 }
 
+#[allow(clippy::print_stdout)]
 impl BenchReporter for JsonReporter {
   fn report_group_summary(&mut self) {}
   #[cold]
@@ -58,7 +59,7 @@ impl BenchReporter for JsonReporter {
   fn report_end(&mut self, _report: &BenchReport) {
     match write_json_to_stdout(self) {
       Ok(_) => (),
-      Err(e) => println!("{e}"),
+      Err(e) => println!("{}", e),
     }
   }
 
@@ -118,6 +119,7 @@ impl ConsoleReporter {
   }
 }
 
+#[allow(clippy::print_stdout)]
 impl BenchReporter for ConsoleReporter {
   #[cold]
   fn report_plan(&mut self, plan: &BenchPlan) {
diff --git a/cli/tools/bundle.rs b/cli/tools/bundle.rs
index 7701b60248..ef058f0d07 100644
--- a/cli/tools/bundle.rs
+++ b/cli/tools/bundle.rs
@@ -125,7 +125,10 @@ async fn bundle_action(
       );
     }
   } else {
-    println!("{}", bundle_output.code);
+    #[allow(clippy::print_stdout)]
+    {
+      println!("{}", bundle_output.code);
+    }
   }
   Ok(())
 }
diff --git a/cli/tools/coverage/reporter.rs b/cli/tools/coverage/reporter.rs
index f86fd186fe..f6f8144a4c 100644
--- a/cli/tools/coverage/reporter.rs
+++ b/cli/tools/coverage/reporter.rs
@@ -103,6 +103,7 @@ struct SummaryCoverageReporter {
   file_reports: Vec<(CoverageReport, String)>,
 }
 
+#[allow(clippy::print_stdout)]
 impl SummaryCoverageReporter {
   pub fn new() -> SummaryCoverageReporter {
     SummaryCoverageReporter {
@@ -166,6 +167,7 @@ impl SummaryCoverageReporter {
   }
 }
 
+#[allow(clippy::print_stdout)]
 impl CoverageReporter for SummaryCoverageReporter {
   fn report(
     &mut self,
@@ -312,6 +314,7 @@ impl DetailedCoverageReporter {
   }
 }
 
+#[allow(clippy::print_stdout)]
 impl CoverageReporter for DetailedCoverageReporter {
   fn report(
     &mut self,
@@ -416,7 +419,7 @@ impl CoverageReporter for HtmlCoverageReporter {
     )
     .unwrap();
 
-    println!("HTML coverage report has been generated at {}", root_report);
+    log::info!("HTML coverage report has been generated at {}", root_report);
   }
 }
 
diff --git a/cli/tools/fmt.rs b/cli/tools/fmt.rs
index b16639f991..ef3d48cb51 100644
--- a/cli/tools/fmt.rs
+++ b/cli/tools/fmt.rs
@@ -396,8 +396,8 @@ async fn format_source_files(
         }
         Err(e) => {
           let _g = output_lock.lock();
-          eprintln!("Error formatting: {}", file_path.to_string_lossy());
-          eprintln!("   {e}");
+          log::error!("Error formatting: {}", file_path.to_string_lossy());
+          log::error!("   {e}");
         }
       }
       Ok(())
@@ -495,6 +495,7 @@ fn format_stdin(fmt_options: FmtOptions, ext: &str) -> Result<(), AnyError> {
   let file_path = PathBuf::from(format!("_stdin.{ext}"));
   let formatted_text = format_file(&file_path, &source, &fmt_options.options)?;
   if fmt_options.check {
+    #[allow(clippy::print_stdout)]
     if formatted_text.is_some() {
       println!("Not formatted stdin");
     }
diff --git a/cli/tools/info.rs b/cli/tools/info.rs
index 7c1d6761a2..19975571b7 100644
--- a/cli/tools/info.rs
+++ b/cli/tools/info.rs
@@ -97,6 +97,7 @@ pub async fn info(flags: Flags, info_flags: InfoFlags) -> Result<(), AnyError> {
   Ok(())
 }
 
+#[allow(clippy::print_stdout)]
 fn print_cache_info(
   factory: &CliFactory,
   json: bool,
diff --git a/cli/tools/jupyter/install.rs b/cli/tools/jupyter/install.rs
index 0c9b8b3e63..69a75837e1 100644
--- a/cli/tools/jupyter/install.rs
+++ b/cli/tools/jupyter/install.rs
@@ -27,13 +27,13 @@ pub fn status() -> Result<(), AnyError> {
   if let Some(specs) = json_output.get("kernelspecs") {
     if let Some(specs_obj) = specs.as_object() {
       if specs_obj.contains_key("deno") {
-        println!("✅ Deno kernel already installed");
+        log::info!("✅ Deno kernel already installed");
         return Ok(());
       }
     }
   }
 
-  println!("ℹ️ Deno kernel is not yet installed, run `deno jupyter --install` to set it up");
+  log::warn!("ℹ️ Deno kernel is not yet installed, run `deno jupyter --install` to set it up");
   Ok(())
 }
 
@@ -108,6 +108,6 @@ pub fn install() -> Result<(), AnyError> {
   }
 
   let _ = std::fs::remove_dir(temp_dir);
-  println!("✅ Deno kernelspec installed successfully.");
+  log::info!("✅ Deno kernelspec installed successfully.");
   Ok(())
 }
diff --git a/cli/tools/jupyter/server.rs b/cli/tools/jupyter/server.rs
index 2107dcfbfc..4021cf6a31 100644
--- a/cli/tools/jupyter/server.rs
+++ b/cli/tools/jupyter/server.rs
@@ -75,7 +75,7 @@ impl JupyterServer {
 
     let handle1 = deno_core::unsync::spawn(async move {
       if let Err(err) = Self::handle_heartbeat(&mut heartbeat).await {
-        eprintln!("Heartbeat error: {}", err);
+        log::error!("Heartbeat error: {}", err);
       }
     });
 
@@ -85,14 +85,14 @@ impl JupyterServer {
         if let Err(err) =
           Self::handle_control(control_socket, cancel_handle).await
         {
-          eprintln!("Control error: {}", err);
+          log::error!("Control error: {}", err);
         }
       }
     });
 
     let handle3 = deno_core::unsync::spawn(async move {
       if let Err(err) = server.handle_shell(shell_socket).await {
-        eprintln!("Shell error: {}", err);
+        log::error!("Shell error: {}", err);
       }
     });
 
@@ -137,7 +137,7 @@ impl JupyterServer {
         .await;
 
       if let Err(err) = result {
-        eprintln!("Output {} error: {}", name, err);
+        log::error!("Output {} error: {}", name, err);
       }
     }
   }
@@ -166,10 +166,10 @@ impl JupyterServer {
           cancel_handle.cancel();
         }
         "interrupt_request" => {
-          eprintln!("Interrupt request currently not supported");
+          log::error!("Interrupt request currently not supported");
         }
         _ => {
-          eprintln!(
+          log::error!(
             "Unrecognized control message type: {}",
             msg.message_type()
           );
@@ -307,7 +307,7 @@ impl JupyterServer {
         // We don't handle these messages
       }
       _ => {
-        eprintln!("Unrecognized shell message type: {}", msg.message_type());
+        log::error!("Unrecognized shell message type: {}", msg.message_type());
       }
     }
 
@@ -386,12 +386,13 @@ impl JupyterServer {
       tokio::time::sleep(std::time::Duration::from_millis(5)).await;
     } else if let Some(exception_details) = exception_details {
       // Determine the exception value and name
-      let (name, message, stack) =
-        if let Some(exception) = exception_details.exception {
-          let result = self
-            .repl_session
-            .call_function_on_args(
-              r#"
+      let (name, message, stack) = if let Some(exception) =
+        exception_details.exception
+      {
+        let result = self
+          .repl_session
+          .call_function_on_args(
+            r#"
           function(object) {
             if (object instanceof Error) {
               const name = "name" in object ? String(object.name) : "";
@@ -404,32 +405,32 @@ impl JupyterServer {
             }
           }
         "#
-              .into(),
-              &[exception],
-            )
-            .await?;
+            .into(),
+            &[exception],
+          )
+          .await?;
 
-          match result.result.value {
-            Some(serde_json::Value::String(str)) => {
-              if let Ok(object) =
-                serde_json::from_str::<HashMap<String, String>>(&str)
-              {
-                let get = |k| object.get(k).cloned().unwrap_or_default();
-                (get("name"), get("message"), get("stack"))
-              } else {
-                eprintln!("Unexpected result while parsing JSON {str}");
-                ("".into(), "".into(), "".into())
-              }
-            }
-            _ => {
-              eprintln!("Unexpected result while parsing exception {result:?}");
+        match result.result.value {
+          Some(serde_json::Value::String(str)) => {
+            if let Ok(object) =
+              serde_json::from_str::<HashMap<String, String>>(&str)
+            {
+              let get = |k| object.get(k).cloned().unwrap_or_default();
+              (get("name"), get("message"), get("stack"))
+            } else {
+              log::error!("Unexpected result while parsing JSON {str}");
               ("".into(), "".into(), "".into())
             }
           }
-        } else {
-          eprintln!("Unexpectedly missing exception {exception_details:?}");
-          ("".into(), "".into(), "".into())
-        };
+          _ => {
+            log::error!("Unexpected result while parsing exception {result:?}");
+            ("".into(), "".into(), "".into())
+          }
+        }
+      } else {
+        log::error!("Unexpectedly missing exception {exception_details:?}");
+        ("".into(), "".into(), "".into())
+      };
 
       let stack = if stack.is_empty() {
         format!(
@@ -546,7 +547,7 @@ async fn publish_result(
   if let Some(exception_details) = &response.exception_details {
     // If the object doesn't have a Jupyter.display method or it throws an
     // exception, we just ignore it and let the caller handle it.
-    eprintln!("Exception encountered: {}", exception_details.text);
+    log::error!("Exception encountered: {}", exception_details.text);
     return Ok(None);
   }
 
diff --git a/cli/tools/lint/mod.rs b/cli/tools/lint/mod.rs
index 03f5b8676e..aeb9199765 100644
--- a/cli/tools/lint/mod.rs
+++ b/cli/tools/lint/mod.rs
@@ -279,6 +279,7 @@ fn collect_lint_files(
     .collect_file_patterns(files)
 }
 
+#[allow(clippy::print_stdout)]
 pub fn print_rules_list(json: bool, maybe_rules_tags: Option<Vec<String>>) {
   let lint_rules = if maybe_rules_tags.is_none() {
     rules::get_all_rules()
@@ -646,12 +647,12 @@ impl LintReporter for PrettyLintReporter {
       }
     }
 
-    eprintln!("{}", d.display());
+    log::error!("{}", d.display());
   }
 
   fn visit_error(&mut self, file_path: &str, err: &AnyError) {
-    eprintln!("Error linting: {file_path}");
-    eprintln!("   {err}");
+    log::error!("Error linting: {file_path}");
+    log::error!("   {err}");
   }
 
   fn close(&mut self, check_count: usize) {
@@ -694,7 +695,7 @@ impl LintReporter for CompactLintReporter {
     match d.range() {
       Some((text_info, range)) => {
         let line_and_column = text_info.line_and_column_display(range.start);
-        eprintln!(
+        log::error!(
           "{}: line {}, col {} - {} ({})",
           d.specifier(),
           line_and_column.line_number,
@@ -704,14 +705,14 @@ impl LintReporter for CompactLintReporter {
         )
       }
       None => {
-        eprintln!("{}: {} ({})", d.specifier(), d.message(), d.code())
+        log::error!("{}: {} ({})", d.specifier(), d.message(), d.code())
       }
     }
   }
 
   fn visit_error(&mut self, file_path: &str, err: &AnyError) {
-    eprintln!("Error linting: {file_path}");
-    eprintln!("   {err}");
+    log::error!("Error linting: {file_path}");
+    log::error!("   {err}");
   }
 
   fn close(&mut self, check_count: usize) {
@@ -812,7 +813,10 @@ impl LintReporter for JsonLintReporter {
   fn close(&mut self, _check_count: usize) {
     sort_diagnostics(&mut self.diagnostics);
     let json = serde_json::to_string_pretty(&self);
-    println!("{}", json.unwrap());
+    #[allow(clippy::print_stdout)]
+    {
+      println!("{}", json.unwrap());
+    }
   }
 }
 
diff --git a/cli/tools/registry/diagnostics.rs b/cli/tools/registry/diagnostics.rs
index 38366ed7ea..31f8157677 100644
--- a/cli/tools/registry/diagnostics.rs
+++ b/cli/tools/registry/diagnostics.rs
@@ -38,7 +38,11 @@ impl PublishDiagnosticsCollector {
     diagnostics.sort_by_cached_key(|d| d.sorting_key());
 
     for diagnostic in diagnostics {
-      eprint!("{}", diagnostic.display());
+      // todo(https://github.com/denoland/deno_ast/issues/245): use log crate here
+      #[allow(clippy::print_stderr)]
+      {
+        eprint!("{}", diagnostic.display());
+      }
       if matches!(diagnostic.level(), DiagnosticLevel::Error) {
         errors += 1;
       }
@@ -48,18 +52,18 @@ impl PublishDiagnosticsCollector {
     }
     if errors > 0 {
       if has_slow_types_errors {
-        eprintln!(
+        log::error!(
           "This package contains errors for slow types. Fixing these errors will:\n"
         );
-        eprintln!(
+        log::error!(
           "  1. Significantly improve your package users' type checking performance."
         );
-        eprintln!("  2. Improve the automatic documentation generation.");
-        eprintln!("  3. Enable automatic .d.ts generation for Node.js.");
-        eprintln!(
+        log::error!("  2. Improve the automatic documentation generation.");
+        log::error!("  3. Enable automatic .d.ts generation for Node.js.");
+        log::error!(
           "\nDon't want to bother? You can choose to skip this step by"
         );
-        eprintln!("providing the --allow-slow-types flag.\n");
+        log::error!("providing the --allow-slow-types flag.\n");
       }
 
       Err(anyhow!(
diff --git a/cli/tools/registry/mod.rs b/cli/tools/registry/mod.rs
index b8d31853b5..1d1e5c54e5 100644
--- a/cli/tools/registry/mod.rs
+++ b/cli/tools/registry/mod.rs
@@ -72,9 +72,10 @@ use super::check::TypeChecker;
 use self::paths::CollectedPublishPath;
 use self::tar::PublishableTarball;
 
+#[allow(clippy::print_stderr)]
 fn ring_bell() {
   // ASCII code for the bell character.
-  print!("\x07");
+  eprint!("\x07");
 }
 
 struct PreparedPublishPackage {
@@ -291,18 +292,19 @@ async fn get_auth_headers(
           .context("Failed to create interactive authorization")?;
 
       let auth_url = format!("{}?code={}", auth.verification_url, auth.code);
-      print!(
-        "Visit {} to authorize publishing of",
-        colors::cyan(&auth_url)
-      );
-      if packages.len() > 1 {
-        println!(" {} packages", packages.len());
+      let pkgs_text = if packages.len() > 1 {
+        format!("{} packages", packages.len())
       } else {
-        println!(" @{}/{}", packages[0].scope, packages[0].package);
-      }
+        format!("@{}/{}", packages[0].scope, packages[0].package)
+      };
+      log::warn!(
+        "Visit {} to authorize publishing of {}",
+        colors::cyan(&auth_url),
+        pkgs_text,
+      );
 
       ring_bell();
-      println!("{}", colors::gray("Waiting..."));
+      log::info!("{}", colors::gray("Waiting..."));
       let _ = open::that_detached(&auth_url);
 
       let interval = std::time::Duration::from_secs(auth.poll_interval);
@@ -323,7 +325,7 @@ async fn get_auth_headers(
             .await;
         match res {
           Ok(res) => {
-            println!(
+            log::info!(
               "{} {} {}",
               colors::green("Authorization successful."),
               colors::gray("Authenticated as"),
@@ -490,13 +492,13 @@ async fn ensure_scopes_and_packages_exist(
     };
 
     ring_bell();
-    println!(
+    log::warn!(
       "'@{}/{}' doesn't exist yet. Visit {} to create the package",
       &package.scope,
       &package.package,
       colors::cyan_with_underline(&create_package_url)
     );
-    println!("{}", colors::gray("Waiting..."));
+    log::warn!("{}", colors::gray("Waiting..."));
     let _ = open::that_detached(&create_package_url);
 
     let package_api_url = api::get_package_api_url(
@@ -510,7 +512,7 @@ async fn ensure_scopes_and_packages_exist(
       let response = client.get(&package_api_url).send().await?;
       if response.status() == 200 {
         let name = format!("@{}/{}", package.scope, package.package);
-        println!("Package {} created", colors::green(name));
+        log::info!("Package {} created", colors::green(name));
         break;
       }
     }
@@ -615,7 +617,7 @@ async fn publish_package(
   provenance: bool,
 ) -> Result<(), AnyError> {
   let client = http_client.client()?;
-  println!(
+  log::info!(
     "{} @{}/{}@{} ...",
     colors::intense_blue("Publishing"),
     package.scope,
@@ -649,7 +651,7 @@ async fn publish_package(
       )
       .unwrap();
       if task.status == "success" {
-        println!(
+        log::info!(
           "{} @{}/{}@{}",
           colors::yellow("Warning: Skipping, already published"),
           package.scope,
@@ -658,7 +660,7 @@ async fn publish_package(
         );
         return Ok(());
       }
-      println!(
+      log::info!(
         "{} @{}/{}@{}",
         colors::yellow("Already uploaded, waiting for publishing"),
         package.scope,
@@ -711,7 +713,7 @@ async fn publish_package(
     );
   }
 
-  println!(
+  log::info!(
     "{} @{}/{}@{}",
     colors::green("Successfully published"),
     package.scope,
@@ -748,7 +750,7 @@ async fn publish_package(
     let bundle = provenance::generate_provenance(subject).await?;
 
     let tlog_entry = &bundle.verification_material.tlog_entries[0];
-    println!("{}",
+    log::info!("{}",
       colors::green(format!(
         "Provenance transparency log available at https://search.sigstore.dev/?logIndex={}",
         tlog_entry.log_index
@@ -768,7 +770,7 @@ async fn publish_package(
       .await?;
   }
 
-  println!(
+  log::info!(
     "{}",
     colors::gray(format!(
       "Visit {}@{}/{}@{} for details",
@@ -798,7 +800,7 @@ async fn prepare_packages_for_publishing(
   let cli_options = cli_factory.cli_options();
 
   if members.len() > 1 {
-    println!("Publishing a workspace...");
+    log::info!("Publishing a workspace...");
   }
 
   // create the module graph
diff --git a/cli/tools/repl/editor.rs b/cli/tools/repl/editor.rs
index 9cb3cd1c26..dbc9bce703 100644
--- a/cli/tools/repl/editor.rs
+++ b/cli/tools/repl/editor.rs
@@ -490,7 +490,7 @@ impl ReplEditor {
         }
 
         self.errored_on_history_save.store(true, Relaxed);
-        eprintln!("Unable to save history file: {e}");
+        log::warn!("Unable to save history file: {}", e);
       }
     }
   }
diff --git a/cli/tools/repl/mod.rs b/cli/tools/repl/mod.rs
index 8847bee52a..c29e29e71f 100644
--- a/cli/tools/repl/mod.rs
+++ b/cli/tools/repl/mod.rs
@@ -40,6 +40,7 @@ struct Repl {
   message_handler: RustylineSyncMessageHandler,
 }
 
+#[allow(clippy::print_stdout)]
 impl Repl {
   async fn run(&mut self) -> Result<(), AnyError> {
     loop {
@@ -61,7 +62,7 @@ impl Repl {
             break;
           }
 
-          println!("{output}");
+          println!("{}", output);
         }
         Err(ReadlineError::Interrupted) => {
           if self.editor.should_exit_on_interrupt() {
@@ -75,7 +76,7 @@ impl Repl {
           break;
         }
         Err(err) => {
-          println!("Error: {err:?}");
+          println!("Error: {:?}", err);
           break;
         }
       }
@@ -85,6 +86,7 @@ impl Repl {
   }
 }
 
+#[allow(clippy::print_stdout)]
 async fn read_line_and_poll(
   repl_session: &mut ReplSession,
   message_handler: &mut RustylineSyncMessageHandler,
@@ -152,6 +154,7 @@ async fn read_eval_file(
   Ok(file.into_text_decoded()?.source)
 }
 
+#[allow(clippy::print_stdout)]
 pub async fn run(flags: Flags, repl_flags: ReplFlags) -> Result<i32, AnyError> {
   let factory = CliFactory::from_flags(flags)?;
   let cli_options = factory.cli_options();
diff --git a/cli/tools/task.rs b/cli/tools/task.rs
index 4d14117d84..63c7f9a946 100644
--- a/cli/tools/task.rs
+++ b/cli/tools/task.rs
@@ -44,7 +44,11 @@ pub async fn execute_script(
   let task_name = match &task_flags.task {
     Some(task) => task,
     None => {
-      print_available_tasks(&tasks_config, &package_json_scripts);
+      print_available_tasks(
+        &mut std::io::stdout(),
+        &tasks_config,
+        &package_json_scripts,
+      )?;
       return Ok(1);
     }
   };
@@ -145,8 +149,14 @@ pub async fn execute_script(
 
     Ok(0)
   } else {
-    eprintln!("Task not found: {task_name}");
-    print_available_tasks(&tasks_config, &package_json_scripts);
+    log::error!("Task not found: {task_name}");
+    if log::log_enabled!(log::Level::Error) {
+      print_available_tasks(
+        &mut std::io::stderr(),
+        &tasks_config,
+        &package_json_scripts,
+      )?;
+    }
     Ok(1)
   }
 }
@@ -239,48 +249,58 @@ fn collect_env_vars() -> HashMap<String, String> {
 }
 
 fn print_available_tasks(
-  // order can be important, so these use an index map
+  writer: &mut dyn std::io::Write,
   tasks_config: &IndexMap<String, deno_config::Task>,
   package_json_scripts: &IndexMap<String, String>,
-) {
-  eprintln!("{}", colors::green("Available tasks:"));
+) -> Result<(), std::io::Error> {
+  writeln!(writer, "{}", colors::green("Available tasks:"))?;
 
-  let mut had_task = false;
-  for (is_deno, (key, task)) in tasks_config
-    .iter()
-    .map(|(k, t)| (true, (k, t.clone())))
-    .chain(
-      package_json_scripts
-        .iter()
-        .filter(|(key, _)| !tasks_config.contains_key(*key))
-        .map(|(k, v)| (false, (k, deno_config::Task::Definition(v.clone())))),
-    )
-  {
-    eprintln!(
-      "- {}{}",
-      colors::cyan(key),
-      if is_deno {
-        "".to_string()
-      } else {
-        format!(" {}", colors::italic_gray("(package.json)"))
-      }
-    );
-    let definition = match &task {
-      deno_config::Task::Definition(definition) => definition,
-      deno_config::Task::Commented { definition, .. } => definition,
-    };
-    if let deno_config::Task::Commented { comments, .. } = &task {
-      let slash_slash = colors::italic_gray("//");
-      for comment in comments {
-        eprintln!("    {slash_slash} {}", colors::italic_gray(comment));
+  if tasks_config.is_empty() && package_json_scripts.is_empty() {
+    writeln!(
+      writer,
+      "  {}",
+      colors::red("No tasks found in configuration file")
+    )?;
+  } else {
+    for (is_deno, (key, task)) in tasks_config
+      .iter()
+      .map(|(k, t)| (true, (k, t.clone())))
+      .chain(
+        package_json_scripts
+          .iter()
+          .filter(|(key, _)| !tasks_config.contains_key(*key))
+          .map(|(k, v)| (false, (k, deno_config::Task::Definition(v.clone())))),
+      )
+    {
+      writeln!(
+        writer,
+        "- {}{}",
+        colors::cyan(key),
+        if is_deno {
+          "".to_string()
+        } else {
+          format!(" {}", colors::italic_gray("(package.json)"))
+        }
+      )?;
+      let definition = match &task {
+        deno_config::Task::Definition(definition) => definition,
+        deno_config::Task::Commented { definition, .. } => definition,
+      };
+      if let deno_config::Task::Commented { comments, .. } = &task {
+        let slash_slash = colors::italic_gray("//");
+        for comment in comments {
+          writeln!(
+            writer,
+            "    {slash_slash} {}",
+            colors::italic_gray(comment)
+          )?;
+        }
       }
+      writeln!(writer, "    {definition}")?;
     }
-    eprintln!("    {definition}");
-    had_task = true;
-  }
-  if !had_task {
-    eprintln!("  {}", colors::red("No tasks found in configuration file"));
   }
+
+  Ok(())
 }
 
 struct NpxCommand;
diff --git a/cli/tools/test/channel.rs b/cli/tools/test/channel.rs
index 780a17de60..a8ce7a9556 100644
--- a/cli/tools/test/channel.rs
+++ b/cli/tools/test/channel.rs
@@ -442,6 +442,8 @@ impl TestEventSender {
   }
 }
 
+#[allow(clippy::print_stdout)]
+#[allow(clippy::print_stderr)]
 #[cfg(test)]
 mod tests {
   use super::*;
diff --git a/cli/tools/test/mod.rs b/cli/tools/test/mod.rs
index 94541cf063..94d4caee01 100644
--- a/cli/tools/test/mod.rs
+++ b/cli/tools/test/mod.rs
@@ -1518,6 +1518,8 @@ pub async fn report_tests(
           &tests,
           &test_steps,
         );
+
+        #[allow(clippy::print_stderr)]
         if let Err(err) = reporter.flush_report(&elapsed, &tests, &test_steps) {
           eprint!("Test reporter failed to flush: {}", err)
         }
diff --git a/cli/tools/test/reporters/dot.rs b/cli/tools/test/reporters/dot.rs
index d2e529a9cd..854ef96660 100644
--- a/cli/tools/test/reporters/dot.rs
+++ b/cli/tools/test/reporters/dot.rs
@@ -11,6 +11,7 @@ pub struct DotTestReporter {
   summary: TestSummary,
 }
 
+#[allow(clippy::print_stdout)]
 impl DotTestReporter {
   pub fn new(cwd: Url) -> DotTestReporter {
     let console_width = if let Some(size) = crate::util::console::console_size()
@@ -80,6 +81,7 @@ fn fmt_cancelled() -> String {
   colors::gray("!").to_string()
 }
 
+#[allow(clippy::print_stdout)]
 impl TestReporter for DotTestReporter {
   fn report_register(&mut self, _description: &TestDescription) {}
 
diff --git a/cli/tools/test/reporters/tap.rs b/cli/tools/test/reporters/tap.rs
index 0758686f03..6dc690e6bd 100644
--- a/cli/tools/test/reporters/tap.rs
+++ b/cli/tools/test/reporters/tap.rs
@@ -22,6 +22,7 @@ pub struct TapTestReporter {
   step_results: HashMap<usize, Vec<(TestStepDescription, TestStepResult)>>,
 }
 
+#[allow(clippy::print_stdout)]
 impl TapTestReporter {
   pub fn new(cwd: Url, is_concurrent: bool) -> TapTestReporter {
     TapTestReporter {
@@ -113,6 +114,7 @@ impl TapTestReporter {
   }
 }
 
+#[allow(clippy::print_stdout)]
 impl TestReporter for TapTestReporter {
   fn report_register(&mut self, _description: &TestDescription) {}
 
diff --git a/cli/tools/upgrade.rs b/cli/tools/upgrade.rs
index 6bb4606d3c..073ebdc1c9 100644
--- a/cli/tools/upgrade.rs
+++ b/cli/tools/upgrade.rs
@@ -274,23 +274,17 @@ pub fn check_for_upgrades(
   if let Some(upgrade_version) = update_checker.should_prompt() {
     if log::log_enabled!(log::Level::Info) && std::io::stderr().is_terminal() {
       if version::is_canary() {
-        eprint!(
-          "{} ",
-          colors::green("A new canary release of Deno is available.")
-        );
-        eprintln!(
-          "{}",
+        log::info!(
+          "{} {}",
+          colors::green("A new canary release of Deno is available."),
           colors::italic_gray("Run `deno upgrade --canary` to install it.")
         );
       } else {
-        eprint!(
-          "{} {} → {} ",
+        log::info!(
+          "{} {} → {} {}",
           colors::green("A new release of Deno is available:"),
           colors::cyan(version::deno()),
-          colors::cyan(&upgrade_version)
-        );
-        eprintln!(
-          "{}",
+          colors::cyan(&upgrade_version),
           colors::italic_gray("Run `deno upgrade` to install it.")
         );
       }
diff --git a/cli/util/file_watcher.rs b/cli/util/file_watcher.rs
index 50ae7c2339..247ae49d8b 100644
--- a/cli/util/file_watcher.rs
+++ b/cli/util/file_watcher.rs
@@ -73,6 +73,7 @@ impl DebouncedReceiver {
   }
 }
 
+#[allow(clippy::print_stderr)]
 async fn error_handler<F>(watch_future: F) -> bool
 where
   F: Future<Output = Result<(), AnyError>>,
@@ -132,8 +133,9 @@ fn create_print_after_restart_fn(
   clear_screen: bool,
 ) -> impl Fn() {
   move || {
+    #[allow(clippy::print_stderr)]
     if clear_screen && std::io::stderr().is_terminal() {
-      eprint!("{CLEAR_SCREEN}");
+      eprint!("{}", CLEAR_SCREEN);
     }
     info!(
       "{} File change detected! Restarting!",
diff --git a/cli/util/v8.rs b/cli/util/v8.rs
index 63bc495d1c..a8ab2c3d0e 100644
--- a/cli/util/v8.rs
+++ b/cli/util/v8.rs
@@ -43,6 +43,8 @@ pub fn init_v8_flags(
     .into_iter()
     .skip(1)
     .collect::<Vec<_>>();
+
+  #[allow(clippy::print_stderr)]
   if !unrecognized_v8_flags.is_empty() {
     for f in unrecognized_v8_flags {
       eprintln!("error: V8 did not recognize flag '{f}'");
diff --git a/cli/worker.rs b/cli/worker.rs
index 302c00e105..a05dff4b23 100644
--- a/cli/worker.rs
+++ b/cli/worker.rs
@@ -868,6 +868,8 @@ fn create_web_worker_callback(
   })
 }
 
+#[allow(clippy::print_stdout)]
+#[allow(clippy::print_stderr)]
 #[cfg(test)]
 mod tests {
   use super::*;
diff --git a/ext/ffi/Cargo.toml b/ext/ffi/Cargo.toml
index 9e6ade702f..8af1b2016c 100644
--- a/ext/ffi/Cargo.toml
+++ b/ext/ffi/Cargo.toml
@@ -19,6 +19,7 @@ dlopen2.workspace = true
 dynasmrt = "1.2.3"
 libffi = "=3.2.0"
 libffi-sys = "=2.3.0"
+log.workspace = true
 serde.workspace = true
 serde-value = "0.7"
 serde_json = "1.0"
diff --git a/ext/ffi/callback.rs b/ext/ffi/callback.rs
index eeea49c239..55f38c6021 100644
--- a/ext/ffi/callback.rs
+++ b/ext/ffi/callback.rs
@@ -176,7 +176,7 @@ unsafe extern "C" fn deno_ffi_callback(
         let tc_scope = &mut TryCatch::new(scope);
         args.run(tc_scope);
         if tc_scope.exception().is_some() {
-          eprintln!("Illegal unhandled exception in nonblocking callback.");
+          log::error!("Illegal unhandled exception in nonblocking callback.");
         }
       });
     }
diff --git a/ext/http/response_body.rs b/ext/http/response_body.rs
index 6b033ffe07..fd1203f53b 100644
--- a/ext/http/response_body.rs
+++ b/ext/http/response_body.rs
@@ -625,6 +625,7 @@ impl PollFrame for BrotliResponseStream {
   }
 }
 
+#[allow(clippy::print_stderr)]
 #[cfg(test)]
 mod tests {
   use super::*;
diff --git a/ext/io/Cargo.toml b/ext/io/Cargo.toml
index 17a9678348..70b5c63f84 100644
--- a/ext/io/Cargo.toml
+++ b/ext/io/Cargo.toml
@@ -18,6 +18,7 @@ async-trait.workspace = true
 deno_core.workspace = true
 filetime.workspace = true
 fs3.workspace = true
+log.workspace = true
 once_cell.workspace = true
 tokio.workspace = true
 
diff --git a/ext/io/winpipe.rs b/ext/io/winpipe.rs
index f66dec6b6b..01d018008d 100644
--- a/ext/io/winpipe.rs
+++ b/ext/io/winpipe.rs
@@ -74,7 +74,7 @@ fn create_named_pipe_inner() -> io::Result<(RawHandle, RawHandle)> {
     // This should not happen, so we would like to get some better diagnostics here.
     // SAFETY: Printing last error for diagnostics
     unsafe {
-      eprintln!(
+      log::error!(
         "*** Unexpected server pipe failure '{pipe_name:?}': {:x}",
         GetLastError()
       );
@@ -99,7 +99,7 @@ fn create_named_pipe_inner() -> io::Result<(RawHandle, RawHandle)> {
     // SAFETY: Getting last error for diagnostics
     let error = unsafe { GetLastError() };
     // This should not happen, so we would like to get some better diagnostics here.
-    eprintln!(
+    log::error!(
       "*** Unexpected client pipe failure '{pipe_name:?}': {:x}",
       error
     );
diff --git a/runtime/examples/extension/main.rs b/runtime/examples/extension/main.rs
index 0026d0de04..0d7c4efb00 100644
--- a/runtime/examples/extension/main.rs
+++ b/runtime/examples/extension/main.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 use std::path::Path;
 use std::rc::Rc;
 
diff --git a/runtime/inspector_server.rs b/runtime/inspector_server.rs
index 8d93819e9f..48d8e0a8fe 100644
--- a/runtime/inspector_server.rs
+++ b/runtime/inspector_server.rs
@@ -176,7 +176,7 @@ fn handle_ws_request(
     let websocket = match fut.await {
       Ok(w) => w,
       Err(err) => {
-        eprintln!(
+        log::error!(
           "Inspector server failed to upgrade to WS connection: {:?}",
           err
         );
@@ -194,7 +194,7 @@ fn handle_ws_request(
       rx: inbound_rx,
     };
 
-    eprintln!("Debugger session started.");
+    log::info!("Debugger session started.");
     let _ = new_session_tx.unbounded_send(inspector_session_proxy);
     pump_websocket_messages(websocket, inbound_tx, outbound_rx).await;
   });
@@ -244,13 +244,13 @@ async fn server(
   let inspector_map = Rc::clone(&inspector_map_);
   let mut register_inspector_handler = pin!(register_inspector_rx
     .map(|info| {
-      eprintln!(
+      log::info!(
         "Debugger listening on {}",
         info.get_websocket_debugger_url(&info.host.to_string())
       );
-      eprintln!("Visit chrome://inspect to connect to the debugger.");
+      log::info!("Visit chrome://inspect to connect to the debugger.");
       if info.wait_for_session {
-        eprintln!("Deno is waiting for debugger to connect.");
+        log::info!("Deno is waiting for debugger to connect.");
       }
       if inspector_map.borrow_mut().insert(info.uuid, info).is_some() {
         panic!("Inspector UUID already in map");
@@ -277,7 +277,7 @@ async fn server(
   let listener = match TcpListener::from_std(listener) {
     Ok(l) => l,
     Err(err) => {
-      eprintln!("Cannot start inspector server: {:?}", err);
+      log::error!("Cannot start inspector server: {:?}", err);
       return;
     }
   };
@@ -293,7 +293,7 @@ async fn server(
           match accept_result {
             Ok((s, _)) => s,
             Err(err) => {
-              eprintln!("Failed to accept inspector connection: {:?}", err);
+              log::error!("Failed to accept inspector connection: {:?}", err);
               continue;
             }
           }
@@ -356,7 +356,7 @@ async fn server(
         tokio::select! {
           result = conn.as_mut() => {
             if let Err(err) = result {
-              eprintln!("Failed to serve connection: {:?}", err);
+              log::error!("Failed to serve connection: {:?}", err);
             }
           },
           _ = &mut shutdown_rx => {
@@ -409,7 +409,7 @@ async fn pump_websocket_messages(
                 OpCode::Close => {
                     // Users don't care if there was an error coming from debugger,
                     // just about the fact that debugger did disconnect.
-                    eprintln!("Debugger session ended");
+                    log::info!("Debugger session ended");
                     break 'pump;
                 }
                 _ => {
diff --git a/runtime/permissions/prompter.rs b/runtime/permissions/prompter.rs
index 42567b1e95..59a3a2f7b0 100644
--- a/runtime/permissions/prompter.rs
+++ b/runtime/permissions/prompter.rs
@@ -280,6 +280,7 @@ impl PermissionPrompter for TtyPrompter {
       return PromptResponse::Deny;
     };
 
+    #[allow(clippy::print_stderr)]
     if message.len() > MAX_PERMISSION_PROMPT_LENGTH {
       eprintln!("❌ Permission prompt length ({} bytes) was larger than the configured maximum length ({} bytes): denying request.", message.len(), MAX_PERMISSION_PROMPT_LENGTH);
       eprintln!("❌ WARNING: This may indicate that code is trying to bypass or hide permission check requests.");
@@ -298,6 +299,7 @@ impl PermissionPrompter for TtyPrompter {
 
     // For security reasons we must consume everything in stdin so that previously
     // buffered data cannot affect the prompt.
+    #[allow(clippy::print_stderr)]
     if let Err(err) = clear_stdin(&mut stdin_lock, &mut stderr_lock) {
       eprintln!("Error clearing stdin for permission prompt. {err:#}");
       return PromptResponse::Deny; // don't grant permission if this fails
@@ -336,6 +338,7 @@ impl PermissionPrompter for TtyPrompter {
       // Clear stdin each time we loop around in case the user accidentally pasted
       // multiple lines or otherwise did something silly to generate a torrent of
       // input. This doesn't work on Windows because `clear_stdin` has other side-effects.
+      #[allow(clippy::print_stderr)]
       #[cfg(unix)]
       if let Err(err) = clear_stdin(&mut stdin_lock, &mut stderr_lock) {
         eprintln!("Error clearing stdin for permission prompt. {err:#}");
diff --git a/runtime/snapshot.rs b/runtime/snapshot.rs
index 2a7d97641e..923ea0b759 100644
--- a/runtime/snapshot.rs
+++ b/runtime/snapshot.rs
@@ -296,6 +296,7 @@ pub fn create_runtime_snapshot(
   let mut snapshot = std::fs::File::create(snapshot_path).unwrap();
   snapshot.write_all(&output.output).unwrap();
 
+  #[allow(clippy::print_stdout)]
   for path in output.files_loaded_during_snapshot {
     println!("cargo:rerun-if-changed={}", path.display());
   }
diff --git a/runtime/tokio_util.rs b/runtime/tokio_util.rs
index da6e8b221a..0d81f6e235 100644
--- a/runtime/tokio_util.rs
+++ b/runtime/tokio_util.rs
@@ -81,8 +81,9 @@ where
       let handle = tokio::runtime::Handle::current();
       let runtime_monitor = RuntimeMonitor::new(&handle);
       tokio::spawn(async move {
+        #[allow(clippy::print_stderr)]
         for interval in runtime_monitor.intervals() {
-          println!("{:#?}", interval);
+          eprintln!("{:#?}", interval);
           // wait 500ms
           tokio::time::sleep(std::time::Duration::from_millis(
             metrics_interval,
diff --git a/runtime/web_worker.rs b/runtime/web_worker.rs
index 27fe633ad4..0124b12a34 100644
--- a/runtime/web_worker.rs
+++ b/runtime/web_worker.rs
@@ -805,6 +805,7 @@ impl WebWorker {
 
         // TODO(mmastrac): we don't want to test this w/classic workers because
         // WPT triggers a failure here. This is only exposed via --enable-testing-features-do-not-use.
+        #[allow(clippy::print_stderr)]
         if self.worker_type == WebWorkerType::Module {
           panic!(
             "coding error: either js is polling or the worker is terminated"
@@ -878,6 +879,7 @@ impl WebWorker {
   }
 }
 
+#[allow(clippy::print_stderr)]
 fn print_worker_error(
   error: &AnyError,
   name: &str,
diff --git a/runtime/worker.rs b/runtime/worker.rs
index ee6b256ff6..a5fec16e47 100644
--- a/runtime/worker.rs
+++ b/runtime/worker.rs
@@ -279,6 +279,7 @@ pub fn create_op_metrics(
       max_len.set(max_len.get().max(decl.name.len()));
       let max_len = max_len.clone();
       Some(Rc::new(
+        #[allow(clippy::print_stderr)]
         move |op: &deno_core::_ops::OpCtx, event, source| {
           eprintln!(
             "[{: >10.3}] {name:max_len$}: {event:?} {source:?}",
@@ -518,7 +519,7 @@ impl MainWorker {
       if !has_notified_of_inspector_disconnect
         .swap(true, std::sync::atomic::Ordering::SeqCst)
       {
-        println!("Program finished. Waiting for inspector to disconnect to exit the process...");
+        log::info!("Program finished. Waiting for inspector to disconnect to exit the process...");
       }
     });
 
diff --git a/tests/ffi/src/lib.rs b/tests/ffi/src/lib.rs
index f6ee31eb88..09c2afb3de 100644
--- a/tests/ffi/src/lib.rs
+++ b/tests/ffi/src/lib.rs
@@ -1,5 +1,7 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
 #![allow(clippy::undocumented_unsafe_blocks)]
 
 use std::os::raw::c_void;
diff --git a/tests/ffi/tests/integration_tests.rs b/tests/ffi/tests/integration_tests.rs
index 0ad95254ce..d0ac6e1049 100644
--- a/tests/ffi/tests/integration_tests.rs
+++ b/tests/ffi/tests/integration_tests.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 use pretty_assertions::assert_eq;
 use std::process::Command;
 use test_util::deno_cmd;
diff --git a/tests/integration/inspector_tests.rs b/tests/integration/inspector_tests.rs
index d18375a831..6a0f9111e1 100644
--- a/tests/integration/inspector_tests.rs
+++ b/tests/integration/inspector_tests.rs
@@ -21,6 +21,7 @@ use test_util as util;
 use tokio::net::TcpStream;
 use tokio::time::timeout;
 use url::Url;
+use util::assert_contains;
 use util::assert_starts_with;
 use util::DenoChild;
 use util::TestContextBuilder;
@@ -94,12 +95,18 @@ impl InspectorTester {
     F: FnMut(&str) -> bool + 'static,
   {
     let stdout = child.stdout.take().unwrap();
-    let stdout_lines =
-      std::io::BufReader::new(stdout).lines().map(|r| r.unwrap());
+    let stdout_lines = std::io::BufReader::new(stdout).lines().map(|r| {
+      let line = r.unwrap();
+      eprintln!("STDOUT: {}", line);
+      line
+    });
 
     let stderr = child.stderr.take().unwrap();
-    let mut stderr_lines =
-      std::io::BufReader::new(stderr).lines().map(|r| r.unwrap());
+    let mut stderr_lines = std::io::BufReader::new(stderr).lines().map(|r| {
+      let line = r.unwrap();
+      eprintln!("STDERR: {}", line);
+      line
+    });
 
     let uri = extract_ws_url_from_stderr(&mut stderr_lines);
 
@@ -810,7 +817,6 @@ async fn inspector_break_on_first_line_in_test() {
   let script = util::testdata_path().join("inspector/inspector_test.js");
   let child = util::deno_cmd()
     .arg("test")
-    .arg("--quiet")
     .arg(inspect_flag_with_unique_port("--inspect-brk"))
     .arg(script)
     .env("NO_COLOR", "1")
@@ -877,10 +883,7 @@ async fn inspector_break_on_first_line_in_test() {
 
   assert_starts_with!(&tester.stdout_line(), "running 1 test from");
   let line = tester.stdout_line();
-  assert!(
-    &line.contains("basic test ... ok"),
-    "Missing content: {line}"
-  );
+  assert_contains!(line, "basic test ... ok");
 
   tester.child.kill().unwrap();
   tester.child.wait().unwrap();
@@ -907,6 +910,7 @@ async fn inspector_with_ts_files() {
   let mut tester = InspectorTester::create(child, notification_filter).await;
 
   tester.assert_stderr_for_inspect_brk();
+  assert_eq!(&tester.stderr_line(), "Debugger session started.");
 
   tester
     .send_many(&[
@@ -926,19 +930,19 @@ async fn inspector_with_ts_files() {
 
   // receive messages with sources from this test
   let script1 = tester.recv().await;
-  assert!(script1.contains("testdata/inspector/test.ts"));
+  assert_contains!(script1, "testdata/inspector/test.ts");
   let script1_id = {
     let v: serde_json::Value = serde_json::from_str(&script1).unwrap();
     v["params"]["scriptId"].as_str().unwrap().to_string()
   };
   let script2 = tester.recv().await;
-  assert!(script2.contains("testdata/inspector/foo.ts"));
+  assert_contains!(script2, "testdata/inspector/foo.ts");
   let script2_id = {
     let v: serde_json::Value = serde_json::from_str(&script2).unwrap();
     v["params"]["scriptId"].as_str().unwrap().to_string()
   };
   let script3 = tester.recv().await;
-  assert!(script3.contains("testdata/inspector/bar.js"));
+  assert_contains!(script3, "testdata/inspector/bar.js");
   let script3_id = {
     let v: serde_json::Value = serde_json::from_str(&script3).unwrap();
     v["params"]["scriptId"].as_str().unwrap().to_string()
@@ -996,10 +1000,12 @@ async fn inspector_with_ts_files() {
     )
     .await;
 
+  let line = tester.stderr_line();
+  assert_contains!(test_util::strip_ansi_codes(&line), "Check");
   assert_eq!(
-      &tester.stdout_line(),
-      "Program finished. Waiting for inspector to disconnect to exit the process..."
-    );
+    &tester.stderr_line(),
+    "Program finished. Waiting for inspector to disconnect to exit the process..."
+  );
 
   tester.child.kill().unwrap();
   tester.child.wait().unwrap();
@@ -1194,7 +1200,6 @@ async fn inspector_break_on_first_line_npm_esm() {
     .new_command()
     .args_vec([
       "run",
-      "--quiet",
       &inspect_flag_with_unique_port("--inspect-brk"),
       "npm:@denotest/bin/cli-esm",
       "this",
@@ -1262,7 +1267,6 @@ async fn inspector_break_on_first_line_npm_cjs() {
     .new_command()
     .args_vec([
       "run",
-      "--quiet",
       &inspect_flag_with_unique_port("--inspect-brk"),
       "npm:@denotest/bin/cli-cjs",
       "this",
@@ -1331,7 +1335,6 @@ async fn inspector_error_with_npm_import() {
     .new_command()
     .args_vec([
       "run",
-      "--quiet",
       "-A",
       &inspect_flag_with_unique_port("--inspect-brk"),
       &script.to_string_lossy(),
@@ -1394,7 +1397,6 @@ async fn inspector_wait() {
     .new_command()
     .args_vec([
       "run",
-      "--quiet",
       "-A",
       &inspect_flag_with_unique_port("--inspect-wait"),
       &script.to_string_lossy(),
diff --git a/tests/integration/mod.rs b/tests/integration/mod.rs
index 30cc9a791b..59bf0db372 100644
--- a/tests/integration/mod.rs
+++ b/tests/integration/mod.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 // These files have `_tests.rs` suffix to make it easier to tell which file is
 // the test (ex. `lint_tests.rs`) and which is the implementation (ex. `lint.rs`)
 // when both are open, especially for two tabs in VS Code
diff --git a/tests/napi/src/lib.rs b/tests/napi/src/lib.rs
index 1b92464835..f6fe6e189a 100644
--- a/tests/napi/src/lib.rs
+++ b/tests/napi/src/lib.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
+
 #![allow(clippy::all)]
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
 #![allow(clippy::undocumented_unsafe_blocks)]
 
 use std::ffi::c_void;
diff --git a/tests/napi/tests/napi_tests.rs b/tests/napi/tests/napi_tests.rs
index 671699651c..1c9b1ba94d 100644
--- a/tests/napi/tests/napi_tests.rs
+++ b/tests/napi/tests/napi_tests.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 use std::process::Command;
 use test_util::deno_cmd;
 use test_util::deno_config_path;
@@ -80,8 +83,8 @@ fn napi_tests() {
 
   if !output.status.success() {
     eprintln!("exit code {:?}", output.status.code());
-    println!("stdout {stdout}");
-    println!("stderr {stderr}");
+    println!("stdout {}", stdout);
+    println!("stderr {}", stderr);
   }
   assert!(output.status.success());
 }
diff --git a/tests/testdata/inspector/inspector_test.js b/tests/testdata/inspector/inspector_test.js
index 86cd48854c..e1ac7b6359 100644
--- a/tests/testdata/inspector/inspector_test.js
+++ b/tests/testdata/inspector/inspector_test.js
@@ -1,3 +1,6 @@
 Deno.test("basic test", () => {
-  console.log("test has finished running");
+  const value = 1 + 1;
+  if (value !== 2) {
+    throw new Error("failed");
+  }
 });
diff --git a/tests/util/server/src/lib.rs b/tests/util/server/src/lib.rs
index ec9154af24..ee5348049d 100644
--- a/tests/util/server/src/lib.rs
+++ b/tests/util/server/src/lib.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 use std::collections::HashMap;
 use std::env;
 use std::io::Write;
diff --git a/tests/util/server/src/test_server.rs b/tests/util/server/src/test_server.rs
index 19e33f9f54..3ae3eaa7d9 100644
--- a/tests/util/server/src/test_server.rs
+++ b/tests/util/server/src/test_server.rs
@@ -1,5 +1,8 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+#![allow(clippy::print_stdout)]
+#![allow(clippy::print_stderr)]
+
 fn main() {
   setup_panic_hook();
   test_server::servers::run_all_servers();
diff --git a/tools/lint.js b/tools/lint.js
index 2bb91f3d56..0fe96b0490 100755
--- a/tools/lint.js
+++ b/tools/lint.js
@@ -162,6 +162,12 @@ async function clippy() {
       "warnings",
       "--deny",
       "clippy::unused_async",
+      // generally prefer the `log` crate, but ignore
+      // these print_* rules if necessary
+      "--deny",
+      "clippy::print_stderr",
+      "--deny",
+      "clippy::print_stdout",
     ],
     stdout: "inherit",
     stderr: "inherit",