diff --git a/pkgs/development/libraries/audio/lilv/default.nix b/pkgs/development/libraries/audio/lilv/default.nix
index a29fda0ec2b2..14b0d4c5e46f 100644
--- a/pkgs/development/libraries/audio/lilv/default.nix
+++ b/pkgs/development/libraries/audio/lilv/default.nix
@@ -20,6 +20,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkg-config python3 wafHook ];
   buildInputs = [ serd sord sratom ];
   propagatedBuildInputs = [ lv2 ];
+  dontAddWafCrossFlags = true;
 
   passthru.tests = {
     inherit pipewire;
diff --git a/pkgs/development/libraries/audio/lv2/default.nix b/pkgs/development/libraries/audio/lv2/default.nix
index d0ef2e65c598..6371a52b4dff 100644
--- a/pkgs/development/libraries/audio/lv2/default.nix
+++ b/pkgs/development/libraries/audio/lv2/default.nix
@@ -22,6 +22,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     pkg-config
     wafHook
+    python3
   ];
 
   buildInputs = [
@@ -35,6 +36,7 @@ stdenv.mkDerivation rec {
   ] ++ lib.optionals stdenv.isDarwin [
     "--lv2dir=${placeholder "out"}/lib/lv2"
   ];
+  dontAddWafCrossFlags = true;
 
   passthru.tests = {
     inherit pipewire;
diff --git a/pkgs/development/libraries/audio/sratom/default.nix b/pkgs/development/libraries/audio/sratom/default.nix
index 1a40d249fd5e..67a66dbfe5a2 100644
--- a/pkgs/development/libraries/audio/sratom/default.nix
+++ b/pkgs/development/libraries/audio/sratom/default.nix
@@ -11,6 +11,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ pkg-config wafHook python3 ];
   buildInputs = [ lv2 serd sord ];
+  dontAddWafCrossFlags = true;
 
   meta = with lib; {
     homepage = "http://drobilla.net/software/sratom";
diff --git a/pkgs/development/tools/build-managers/wafHook/setup-hook.sh b/pkgs/development/tools/build-managers/wafHook/setup-hook.sh
index 6cea8fcc2ea8..e2f6714a32d4 100644
--- a/pkgs/development/tools/build-managers/wafHook/setup-hook.sh
+++ b/pkgs/development/tools/build-managers/wafHook/setup-hook.sh
@@ -10,6 +10,10 @@ wafConfigurePhase() {
         wafConfigureFlags="${prefixKey:---prefix=}$prefix $wafConfigureFlags"
     fi
 
+    if [ -n "${PKG_CONFIG}" ]; then
+      export PKGCONFIG="${PKG_CONFIG}"
+    fi
+
     local flagsArray=(
         "${flagsArray[@]}"
         $wafConfigureFlags "${wafConfigureFlagsArray[@]}"
diff --git a/pkgs/misc/jackaudio/default.nix b/pkgs/misc/jackaudio/default.nix
index 92574231549e..2f7ffeb89f32 100644
--- a/pkgs/misc/jackaudio/default.nix
+++ b/pkgs/misc/jackaudio/default.nix
@@ -48,8 +48,6 @@ stdenv.mkDerivation rec {
         --replace /bin/bash ${bash}/bin/bash
   '';
 
-  PKGCONFIG = "${stdenv.cc.targetPrefix}pkg-config";
-
   dontAddWafCrossFlags = "true";
   wafConfigureFlags = [
     "--classic"