diff --git a/pkgs/applications/editors/bluej/default.nix b/pkgs/applications/editors/bluej/default.nix
index bfc413c24ad4..552358319e15 100644
--- a/pkgs/applications/editors/bluej/default.nix
+++ b/pkgs/applications/editors/bluej/default.nix
@@ -50,7 +50,7 @@ stdenv.mkDerivation rec {
   preFixup = ''
     makeWrapper ${jdk}/bin/java $out/bin/bluej \
       "''${gappsWrapperArgs[@]}" \
-      --add-flags "-Djavafx.embed.singleThread=true -Dawt.useSystemAAFontSettings=on -Xmx512M -cp \"$out/share/bluej/bluej.jar\" bluej.Boot"
+      --add-flags "-Djavafx.embed.singleThread=true -Dawt.useSystemAAFontSettings=on -Xmx512M -cp $out/share/bluej/bluej.jar bluej.Boot"
   '';
 
   meta = with lib; {
diff --git a/pkgs/applications/editors/vscode/generic.nix b/pkgs/applications/editors/vscode/generic.nix
index 9a4f1b92d41f..e10031800502 100644
--- a/pkgs/applications/editors/vscode/generic.nix
+++ b/pkgs/applications/editors/vscode/generic.nix
@@ -1,5 +1,5 @@
 { stdenv, lib, makeDesktopItem
-, unzip, libsecret, libXScrnSaver, libxshmfence, wrapGAppsHook
+, unzip, libsecret, libXScrnSaver, libxshmfence, wrapGAppsHook, makeWrapper
 , atomEnv, at-spi2-atk, autoPatchelfHook
 , systemd, fontconfig, libdbusmenu, glib, buildFHSUserEnvBubblewrap
 , writeShellScriptBin
@@ -68,7 +68,12 @@ let
 
     runtimeDependencies = lib.optional stdenv.isLinux [ (lib.getLib systemd) fontconfig.lib libdbusmenu ];
 
-    nativeBuildInputs = [ unzip ] ++ lib.optionals stdenv.isLinux [ autoPatchelfHook nodePackages.asar wrapGAppsHook ];
+    nativeBuildInputs = [ unzip ]
+      ++ lib.optionals stdenv.isLinux [
+        autoPatchelfHook
+        nodePackages.asar
+        (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
+      ];
 
     dontBuild = true;
     dontConfigure = true;
diff --git a/pkgs/applications/misc/gmtp/default.nix b/pkgs/applications/misc/gmtp/default.nix
index 1479fe7bc7d8..5f03b8ea7e76 100644
--- a/pkgs/applications/misc/gmtp/default.nix
+++ b/pkgs/applications/misc/gmtp/default.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation {
   enableParallelBuilding = true;
 
   preFixup = ''
-    gappsWrapperArgs+=(--add-flags "--datapath \"$out/share\"");
+    gappsWrapperArgs+=(--add-flags "--datapath $out/share");
   '';
 
   meta = {
diff --git a/pkgs/applications/networking/browsers/brave/default.nix b/pkgs/applications/networking/browsers/brave/default.nix
index b216d750d562..79b9b498fbd7 100644
--- a/pkgs/applications/networking/browsers/brave/default.nix
+++ b/pkgs/applications/networking/browsers/brave/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, wrapGAppsHook
+{ lib, stdenv, fetchurl, wrapGAppsHook, makeWrapper
 , dpkg
 , alsa-lib
 , at-spi2-atk
@@ -102,7 +102,10 @@ stdenv.mkDerivation rec {
   dontPatchELF = true;
   doInstallCheck = true;
 
-  nativeBuildInputs = [ dpkg wrapGAppsHook ];
+  nativeBuildInputs = [
+    dpkg
+    (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
+  ];
 
   buildInputs = [
     # needed for GSETTINGS_SCHEMAS_PATH
diff --git a/pkgs/applications/networking/instant-messengers/discord/linux.nix b/pkgs/applications/networking/instant-messengers/discord/linux.nix
index 05833c1eeaf4..f5d984bf3a67 100644
--- a/pkgs/applications/networking/instant-messengers/discord/linux.nix
+++ b/pkgs/applications/networking/instant-messengers/discord/linux.nix
@@ -1,5 +1,5 @@
 { pname, version, src, meta, binaryName, desktopName, autoPatchelfHook
-, makeDesktopItem, lib, stdenv, wrapGAppsHook, alsa-lib, at-spi2-atk
+, makeDesktopItem, lib, stdenv, wrapGAppsHook, makeWrapper, alsa-lib, at-spi2-atk
 , at-spi2-core, atk, cairo, cups, dbus, expat, fontconfig, freetype, gdk-pixbuf
 , glib, gtk3, libcxx, libdrm, libnotify, libpulseaudio, libuuid, libX11
 , libXScrnSaver, libXcomposite, libXcursor, libXdamage, libXext, libXfixes
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
     libxshmfence
     mesa
     nss
-    wrapGAppsHook
+    (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
   ];
 
   dontWrapGApps = true;
diff --git a/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix b/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
index 6afccfaaa070..96c6809b0453 100644
--- a/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, autoPatchelfHook, dpkg, wrapGAppsHook, nixosTests
+{ stdenv, lib, fetchurl, autoPatchelfHook, dpkg, wrapGAppsHook, makeWrapper, nixosTests
 , gtk3, atk, at-spi2-atk, cairo, pango, gdk-pixbuf, glib, freetype, fontconfig
 , dbus, libX11, xorg, libXi, libXcursor, libXdamage, libXrandr, libXcomposite
 , libXext, libXfixes, libXrender, libXtst, libXScrnSaver, nss, nspr, alsa-lib
@@ -40,7 +40,7 @@ in stdenv.mkDerivation rec {
   nativeBuildInputs = [
     autoPatchelfHook
     dpkg
-    wrapGAppsHook
+    (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
   ];
 
   buildInputs = [
diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix
index e13fd578927d..d84f0b2abf69 100644
--- a/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix
@@ -34,7 +34,10 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gtk3 ];
 
-  nativeBuildInputs = [ makeWrapper wrapGAppsHook ];
+  nativeBuildInputs = [
+    makeWrapper
+    (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
+  ];
 
   dontWrapGApps = true;
 
diff --git a/pkgs/tools/security/cryptomator/default.nix b/pkgs/tools/security/cryptomator/default.nix
index 76b5f5216636..5a1886e49e55 100644
--- a/pkgs/tools/security/cryptomator/default.nix
+++ b/pkgs/tools/security/cryptomator/default.nix
@@ -98,7 +98,13 @@ in stdenv.mkDerivation rec {
     cp ${src}/dist/linux/common/application-vnd.cryptomator.vault.xml $out/share/mime/packages/application-vnd.cryptomator.vault.xml
   '';
 
-  nativeBuildInputs = [ autoPatchelfHook maven makeWrapper wrapGAppsHook jdk ];
+  nativeBuildInputs = [
+    autoPatchelfHook
+    maven
+    makeWrapper
+    (wrapGAppsHook.override { makeBinaryWrapper = makeWrapper; })
+    jdk
+  ];
   buildInputs = [ fuse jre glib jffi ];
 
   meta = with lib; {