diff --git a/build-aux/flatpak/org.gnome.Nautilus.json b/build-aux/flatpak/org.gnome.Nautilus.json
index d2dd12232..75200d13a 100644
--- a/build-aux/flatpak/org.gnome.Nautilus.json
+++ b/build-aux/flatpak/org.gnome.Nautilus.json
@@ -85,22 +85,19 @@
                 "/etc",
                 "/libexec"
             ],
+            "buildsystem": "meson",
+            "builddir": "true",
             "config-opts" : [
-                "--disable-miner-apps",
-                "--disable-static",
-                "--disable-tracker-extract",
-                "--disable-tracker-needle",
-                "--disable-tracker-preferences",
-                "--disable-artwork",
-                "--disable-tracker-writeback",
-                "--disable-miner-user-guides",
-                "--with-bash-completion-dir=no"
+                "-Ddocs=false",
+                "-Dbash_completion=no",
+                "-Ddbus_services=no",
+                "--prefix=/app",
+                "--libdir=/app/lib"
             ],
             "sources" : [
                 {
                     "type" : "git",
-                    "url" : "https://gitlab.gnome.org/GNOME/tracker.git",
-                    "tag" : "2.0.3"
+                    "url" : "https://gitlab.gnome.org/GNOME/tracker.git"
                 }
             ]
         },
@@ -134,4 +131,4 @@
         "env" : {
         }
     }
-}
+}
\ No newline at end of file
diff --git a/build-aux/flatpak/org.gnome.Nautilus.yml b/build-aux/flatpak/org.gnome.Nautilus.yml
index edd3c76b7..53d91a4f7 100644
--- a/build-aux/flatpak/org.gnome.Nautilus.yml
+++ b/build-aux/flatpak/org.gnome.Nautilus.yml
@@ -66,21 +66,18 @@ modules:
       - /bin
       - /etc
       - /libexec
+    buildsystem: meson
+    builddir: true
     build-options:
       config-opts:
-        - --disable-miner-apps
-        - --disable-static
-        - --disable-tracker-extract
-        - --disable-tracker-needle
-        - --disable-tracker-preferences
-        - --disable-artwork
-        - --disable-tracker-writeback
-        - --disable-miner-user-guides
-        - --with-bash-completion-dir=no
+        - -Ddocs=false
+        - -Dbash_completion=no
+        - -Ddbus_services=no
+        - --prefix=/app
+        - --libdir=/app/lib
     sources:
       - type: git
         url: https://gitlab.gnome.org/GNOME/tracker.git
-        tag: 2.0.3
 
   - name: gnome-autoar
     sources:
diff --git a/build-aux/flatpak/org.gnome.NautilusGtk4.yml b/build-aux/flatpak/org.gnome.NautilusGtk4.yml
index f833e8cc9..b8caf8a24 100644
--- a/build-aux/flatpak/org.gnome.NautilusGtk4.yml
+++ b/build-aux/flatpak/org.gnome.NautilusGtk4.yml
@@ -52,17 +52,22 @@ modules:
         url: "https://gitlab.gnome.org/GNOME/gexiv2.git"
 
   - name: "tracker"
+    cleanup:
+    - /bin
+    - /etc
+    - /libexec
+    buildsystem: meson
+    builddir: true
     build-options:
       config-opts:
-        - "-Ddocs=false"
-        - "-Dfunctional_tests=false"
-        - "-Dbash_completion=no"
-        - "-Ddbus_services=no"
+        - -Ddocs=false
+        - -Dbash_completion=no
+        - -Ddbus_services=no
+        - --prefix=/app
+        - --libdir=/app/lib
     sources:
       - type: "git"
         url: "https://gitlab.gnome.org/GNOME/tracker.git"
-    buildsystem: "meson"
-    builddir: true
 
   - name: "gnome-autoar"
     sources:
diff --git a/build-aux/flatpak/org.gnome.NautilusMaster.yml b/build-aux/flatpak/org.gnome.NautilusMaster.yml
index 94da69f77..35fd22888 100644
--- a/build-aux/flatpak/org.gnome.NautilusMaster.yml
+++ b/build-aux/flatpak/org.gnome.NautilusMaster.yml
@@ -55,17 +55,15 @@ modules:
       - /bin
       - /etc
       - /libexec
+    buildsystem: meson
+    builddir: true
     build-options:
       config-opts:
-        - --disable-miner-apps
-        - --disable-static
-        - --disable-tracker-extract
-        - --disable-tracker-needle
-        - --disable-tracker-preferences
-        - --disable-artwork
-        - --disable-tracker-writeback
-        - --disable-miner-user-guides
-        - --with-bash-completion-dir=no
+        - -Ddocs=false
+        - -Dbash_completion=no
+        - -Ddbus_services=no
+        - --prefix=/app
+        - --libdir=/app/lib
     sources:
       - type: git
         url: https://gitlab.gnome.org/GNOME/tracker.git