diff --git a/builtin/apply.c b/builtin/apply.c
index 6013e1913c..4270cded0b 100644
--- a/builtin/apply.c
+++ b/builtin/apply.c
@@ -1920,6 +1920,23 @@ static int parse_binary(char *buffer, unsigned long size, struct patch *patch)
 	return used;
 }
 
+static void prefix_one(char **name)
+{
+	char *old_name = *name;
+	if (!old_name)
+		return;
+	*name = xstrdup(prefix_filename(prefix, prefix_length, *name));
+	free(old_name);
+}
+
+static void prefix_patch(struct patch *p)
+{
+	if (!prefix || p->is_toplevel_relative)
+		return;
+	prefix_one(&p->new_name);
+	prefix_one(&p->old_name);
+}
+
 /*
  * Read the patch text in "buffer" that extends for "size" bytes; stop
  * reading after seeing a single patch (i.e. changes to a single file).
@@ -1935,6 +1952,8 @@ static int parse_chunk(char *buffer, unsigned long size, struct patch *patch)
 	if (offset < 0)
 		return offset;
 
+	prefix_patch(patch);
+
 	patch->ws_rule = whitespace_rule(patch->new_name
 					 ? patch->new_name
 					 : patch->old_name);
@@ -4164,26 +4183,6 @@ static int use_patch(struct patch *p)
 	return !has_include;
 }
 
-
-static void prefix_one(char **name)
-{
-	char *old_name = *name;
-	if (!old_name)
-		return;
-	*name = xstrdup(prefix_filename(prefix, prefix_length, *name));
-	free(old_name);
-}
-
-static void prefix_patches(struct patch *p)
-{
-	if (!prefix || p->is_toplevel_relative)
-		return;
-	for ( ; p; p = p->next) {
-		prefix_one(&p->new_name);
-		prefix_one(&p->old_name);
-	}
-}
-
 #define INACCURATE_EOF	(1<<0)
 #define RECOUNT		(1<<1)
 
@@ -4209,8 +4208,6 @@ static int apply_patch(int fd, const char *filename, int options)
 			break;
 		if (apply_in_reverse)
 			reverse_patches(patch);
-		if (prefix)
-			prefix_patches(patch);
 		if (use_patch(patch)) {
 			patch_stats(patch);
 			*listp = patch;
diff --git a/t/t4119-apply-config.sh b/t/t4119-apply-config.sh
index 3d0384daa8..be325fa1ae 100755
--- a/t/t4119-apply-config.sh
+++ b/t/t4119-apply-config.sh
@@ -159,4 +159,21 @@ test_expect_success 'same but with traditional patch input of depth 2' '
 	check_result sub/file1
 '
 
+test_expect_success 'in subdir with traditional patch input' '
+	cd "$D" &&
+	git config apply.whitespace strip &&
+	cat >.gitattributes <<-EOF &&
+	/* whitespace=blank-at-eol
+	sub/* whitespace=-blank-at-eol
+	EOF
+	rm -f sub/file1 &&
+	cp saved sub/file1 &&
+	git update-index --refresh &&
+
+	cd sub &&
+	git apply ../gpatch.file &&
+	echo "B " >expect &&
+	test_cmp expect file1
+'
+
 test_done