diff --git a/pkgs/applications/audio/rhythmbox/default.nix b/pkgs/applications/audio/rhythmbox/default.nix
index 394ccc3b723d..9929a32aabbf 100644
--- a/pkgs/applications/audio/rhythmbox/default.nix
+++ b/pkgs/applications/audio/rhythmbox/default.nix
@@ -101,7 +101,7 @@ stdenv.mkDerivation rec {
 
   preFixup = ''
     gappsWrapperArgs+=(
-      --prefix PYTHONPATH : "${python3.pkgs.pygobject3}/${python3.sitePackages}:$out/lib/rhythmbox/plugins/"
+      --prefix PYTHONPATH : "$out/lib/rhythmbox/plugins/"
     )
   '';
 
diff --git a/pkgs/applications/editors/gnome-builder/default.nix b/pkgs/applications/editors/gnome-builder/default.nix
index fc3f3fd27474..da36d5f111f7 100644
--- a/pkgs/applications/editors/gnome-builder/default.nix
+++ b/pkgs/applications/editors/gnome-builder/default.nix
@@ -73,7 +73,6 @@ stdenv.mkDerivation rec {
     ninja
     pkg-config
     python3
-    python3.pkgs.wrapPython
     wrapGAppsHook4
   ];
 
@@ -137,12 +136,8 @@ stdenv.mkDerivation rec {
       meson test --print-errorlogs
   '';
 
-  pythonPath = with python3.pkgs; requiredPythonModules [ pygobject3 ];
-
   preFixup = ''
-    buildPythonPath "$out $pythonPath"
     gappsWrapperArgs+=(
-      --prefix PYTHONPATH : "$program_PYTHONPATH"
       # For sysprof-agent
       --prefix PATH : "${sysprof}/bin"
     )
diff --git a/pkgs/applications/networking/mailreaders/astroid/default.nix b/pkgs/applications/networking/mailreaders/astroid/default.nix
index 739f45fd4ee9..518d47a9a40a 100644
--- a/pkgs/applications/networking/mailreaders/astroid/default.nix
+++ b/pkgs/applications/networking/mailreaders/astroid/default.nix
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     sed -i "s~ -geom 10x10~~g" src/config.cc
   '';
 
-  pythonPath = with python3.pkgs; requiredPythonModules [ pygobject3 ] ++ extraPythonPackages;
+  pythonPath = with python3.pkgs; requiredPythonModules extraPythonPackages;
   preFixup = ''
     buildPythonPath "$out $pythonPath"
     gappsWrapperArgs+=(
diff --git a/pkgs/applications/networking/newsreaders/liferea/default.nix b/pkgs/applications/networking/newsreaders/liferea/default.nix
index d7643a6f07e8..0851d0f30e79 100644
--- a/pkgs/applications/networking/newsreaders/liferea/default.nix
+++ b/pkgs/applications/networking/newsreaders/liferea/default.nix
@@ -73,14 +73,9 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  pythonPath = with python3Packages; [
-    pygobject3
-    pycairo
-  ];
-
-  preFixup = ''
-    buildPythonPath "$out $pythonPath"
-    gappsWrapperArgs+=(--prefix PYTHONPATH : "$program_PYTHONPATH")
+  postFixup = ''
+    buildPythonPath ${python3Packages.pycairo}
+    patchPythonScript $out/lib/liferea/plugins/trayicon.py
   '';
 
   passthru.updateScript = gitUpdater {
diff --git a/pkgs/applications/video/xplayer/default.nix b/pkgs/applications/video/xplayer/default.nix
index 20a9772021a9..baa8fcb95be0 100644
--- a/pkgs/applications/video/xplayer/default.nix
+++ b/pkgs/applications/video/xplayer/default.nix
@@ -25,13 +25,6 @@
 , xapp
 , yelp-tools }:
 
-let
-  pythonenv = python3.withPackages (ps: [
-    ps.pygobject3
-    ps.dbus-python # For one plugin
-  ]);
-in
-
 stdenv.mkDerivation rec {
   pname = "xplayer";
   version = "2.4.4";
@@ -66,6 +59,7 @@ stdenv.mkDerivation rec {
     intltool
     itstool
     pkg-config
+    python3.pkgs.wrapPython
     yelp-tools
     gobject-introspection
   ];
@@ -82,15 +76,15 @@ stdenv.mkDerivation rec {
     libpeas
     libxml2
     libxplayer-plparser
-    pythonenv
+    python3
     xapp
     # to satisfy configure script
-    pythonenv.pkgs.pygobject3
+    python3.pkgs.pygobject3
   ];
 
-  postInstall = ''
-    wrapProgram $out/bin/xplayer \
-                --prefix PATH : ${lib.makeBinPath [ pythonenv ]}
+  postFixup = ''
+    buildPythonPath ${python3.pkgs.dbus-python}
+    patchPythonScript $out/lib/xplayer/plugins/dbus/dbusservice.py
   '';
 
   meta = with lib; {
diff --git a/pkgs/desktops/gnome/core/totem/default.nix b/pkgs/desktops/gnome/core/totem/default.nix
index 24c637909a32..1f6755002f01 100644
--- a/pkgs/desktops/gnome/core/totem/default.nix
+++ b/pkgs/desktops/gnome/core/totem/default.nix
@@ -91,9 +91,7 @@ stdenv.mkDerivation rec {
     adwaita-icon-theme
     gnome-desktop
     gsettings-desktop-schemas
-    # for plug-ins
     python3Packages.pygobject3
-    python3Packages.dbus-python
   ];
 
   nativeCheckInputs = [
@@ -124,8 +122,6 @@ stdenv.mkDerivation rec {
     runHook postCheck
   '';
 
-  wrapPrefixVariables = [ "PYTHONPATH" ];
-
   passthru = {
     updateScript = gnome.updateScript {
       packageName = "totem";
diff --git a/pkgs/desktops/mate/pluma/default.nix b/pkgs/desktops/mate/pluma/default.nix
index 665e1b49a436..ed7d54e9469b 100644
--- a/pkgs/desktops/mate/pluma/default.nix
+++ b/pkgs/desktops/mate/pluma/default.nix
@@ -32,6 +32,7 @@ stdenv.mkDerivation rec {
     itstool
     perl
     pkg-config
+    python3.pkgs.wrapPython
     wrapGAppsHook
   ];
 
@@ -47,6 +48,16 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  pythonPath = with python3.pkgs; [
+    pycairo
+    six
+  ];
+
+  postFixup = ''
+    buildPythonPath "$pythonPath"
+    patchPythonScript $out/lib/pluma/plugins/snippets/Snippet.py
+  '';
+
   passthru.updateScript = mateUpdateScript { inherit pname; };
 
   meta = with lib; {
diff --git a/pkgs/development/libraries/libpeas/2.x.nix b/pkgs/development/libraries/libpeas/2.x.nix
index 547d7f5c27ef..38e4fe055085 100644
--- a/pkgs/development/libraries/libpeas/2.x.nix
+++ b/pkgs/development/libraries/libpeas/2.x.nix
@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , fetchurl
+, substituteAll
 , pkg-config
 , gi-docgen
 , gobject-introspection
@@ -25,6 +26,16 @@ stdenv.mkDerivation rec {
     hash = "sha256-ndwdUfOGY9pN9SFjBRt7LOo6JCz67p9afhQPB4TIqnc=";
   };
 
+  patches = [
+    # Make PyGObject’s gi library available.
+    (substituteAll {
+      src = ./fix-paths.patch;
+      pythonPaths = lib.concatMapStringsSep ", " (pkg: "'${pkg}/${python3.sitePackages}'") [
+        python3.pkgs.pygobject3
+      ];
+    })
+  ];
+
   depsBuildBuild = [
     pkg-config
   ];
diff --git a/pkgs/development/libraries/libpeas/default.nix b/pkgs/development/libraries/libpeas/default.nix
index 70d33d86ad19..f0b6023117d9 100644
--- a/pkgs/development/libraries/libpeas/default.nix
+++ b/pkgs/development/libraries/libpeas/default.nix
@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , fetchurl
+, substituteAll
 , meson
 , ninja
 , pkg-config
@@ -12,6 +13,7 @@
 , gobject-introspection
 , python3
 , ncurses
+, wrapGAppsHook
 }:
 
 stdenv.mkDerivation rec {
@@ -25,6 +27,16 @@ stdenv.mkDerivation rec {
     sha256 = "KXy5wszNjoYXYj0aPoQVtFMLjlqJPjUnu/0e3RMje0w=";
   };
 
+  patches = [
+    # Make PyGObject’s gi library available.
+    (substituteAll {
+      src = ./fix-paths.patch;
+      pythonPaths = lib.concatMapStringsSep ", " (pkg: "'${pkg}/${python3.sitePackages}'") [
+        python3.pkgs.pygobject3
+      ];
+    })
+  ];
+
   depsBuildBuild = [
     pkg-config
   ];
@@ -36,6 +48,7 @@ stdenv.mkDerivation rec {
     gettext
     gi-docgen
     gobject-introspection
+    wrapGAppsHook
   ];
 
   buildInputs = [
diff --git a/pkgs/development/libraries/libpeas/fix-paths.patch b/pkgs/development/libraries/libpeas/fix-paths.patch
new file mode 100644
index 000000000000..c54cdd8873f5
--- /dev/null
+++ b/pkgs/development/libraries/libpeas/fix-paths.patch
@@ -0,0 +1,14 @@
+diff --git a/loaders/python/peas-plugin-loader-python.c b/loaders/python/peas-plugin-loader-python.c
+index 26edbf3..0d65ada 100644
+--- a/loaders/python/peas-plugin-loader-python.c
++++ b/loaders/python/peas-plugin-loader-python.c
+@@ -248,6 +248,9 @@ peas_plugin_loader_python_initialize (PeasPluginLoader *loader)
+       goto python_init_error;
+     }
+ 
++  /* Add PyGObject to path */
++  PyRun_SimpleString("import site; import functools; functools.reduce(lambda k, p: site.addsitedir(p, k), [@pythonPaths@], site._init_pathinfo())");
++
+   /* Initialize PyGObject */
+   pygobject_init (PYGOBJECT_MAJOR_VERSION,
+                   PYGOBJECT_MINOR_VERSION,