diff --git a/pkgs/applications/editors/mg/default.nix b/pkgs/applications/editors/mg/default.nix
index 612cdcc7f88..ef6943001b9 100644
--- a/pkgs/applications/editors/mg/default.nix
+++ b/pkgs/applications/editors/mg/default.nix
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  makeFlags = [ "PKG_CONFIG=${buildPackages.pkgconfig}/bin/pkg-config" ];
+  makeFlags = [ "PKG_CONFIG=${buildPackages.pkgconfig}/bin/${buildPackages.pkgconfig.targetPrefix}pkg-config" ];
 
   installPhase = ''
     install -m 555 -Dt $out/bin mg
diff --git a/pkgs/applications/graphics/ImageMagick/7.0.nix b/pkgs/applications/graphics/ImageMagick/7.0.nix
index f2542301119..cbc72f91dcc 100644
--- a/pkgs/applications/graphics/ImageMagick/7.0.nix
+++ b/pkgs/applications/graphics/ImageMagick/7.0.nix
@@ -71,7 +71,7 @@ stdenv.mkDerivation {
     moveToOutput "lib/ImageMagick-*/config-Q16HDRI" "$dev" # includes configure params
     for file in "$dev"/bin/*-config; do
       substituteInPlace "$file" --replace pkg-config \
-        "PKG_CONFIG_PATH='$dev/lib/pkgconfig' '${pkgconfig}/bin/pkg-config'"
+        "PKG_CONFIG_PATH='$dev/lib/pkgconfig' '${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config'"
     done
   '' + lib.optionalString (ghostscript != null) ''
     for la in $out/lib/*.la; do
diff --git a/pkgs/applications/graphics/ImageMagick/default.nix b/pkgs/applications/graphics/ImageMagick/default.nix
index 0ded57b1a72..583a845c3c7 100644
--- a/pkgs/applications/graphics/ImageMagick/default.nix
+++ b/pkgs/applications/graphics/ImageMagick/default.nix
@@ -85,9 +85,9 @@ stdenv.mkDerivation {
     moveToOutput "lib/ImageMagick-*/config-Q16" "$dev" # includes configure params
     for file in "$dev"/bin/*-config; do
       substituteInPlace "$file" --replace "${pkgconfig}/bin/pkg-config -config" \
-        ${pkgconfig}/bin/pkg-config
+        ${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config
       substituteInPlace "$file" --replace ${pkgconfig}/bin/pkg-config \
-        "PKG_CONFIG_PATH='$dev/lib/pkgconfig' '${pkgconfig}/bin/pkg-config'"
+        "PKG_CONFIG_PATH='$dev/lib/pkgconfig' '${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config'"
     done
   '' + lib.optionalString (ghostscript != null) ''
     for la in $out/lib/*.la; do
diff --git a/pkgs/applications/misc/stupidterm/default.nix b/pkgs/applications/misc/stupidterm/default.nix
index 0a6e947f15c..2016059d81e 100644
--- a/pkgs/applications/misc/stupidterm/default.nix
+++ b/pkgs/applications/misc/stupidterm/default.nix
@@ -15,7 +15,7 @@ stdenv.mkDerivation {
     sha256 = "1f73wvqqvj5pr3fvb7jjc4bi1iwgkkknz24k8n69mdb75jnfjipp";
   };
 
-  makeFlags = [ "PKGCONFIG=${pkgconfig}/bin/pkg-config" "binary=stupidterm" ];
+  makeFlags = [ "PKGCONFIG=${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config" "binary=stupidterm" ];
 
   installPhase = ''
     install -D stupidterm $out/bin/stupidterm
diff --git a/pkgs/build-support/dotnetbuildhelpers/default.nix b/pkgs/build-support/dotnetbuildhelpers/default.nix
index 0edfd0b467a..809619ed55d 100644
--- a/pkgs/build-support/dotnetbuildhelpers/default.nix
+++ b/pkgs/build-support/dotnetbuildhelpers/default.nix
@@ -12,7 +12,7 @@
         cp -v "$script" "$target"/"$scriptName"
         chmod 755 "$target"/"$scriptName"
         patchShebangs "$target"/"$scriptName"
-        substituteInPlace "$target"/"$scriptName" --replace pkg-config ${pkgconfig}/bin/pkg-config
+        substituteInPlace "$target"/"$scriptName" --replace pkg-config ${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config
         substituteInPlace "$target"/"$scriptName" --replace monodis ${mono}/bin/monodis
       done
     ''
diff --git a/pkgs/development/libraries/ffmpeg/generic.nix b/pkgs/development/libraries/ffmpeg/generic.nix
index f56447668ea..881166ef9b9 100644
--- a/pkgs/development/libraries/ffmpeg/generic.nix
+++ b/pkgs/development/libraries/ffmpeg/generic.nix
@@ -163,7 +163,6 @@ stdenv.mkDerivation rec {
   ] ++ optionals (stdenv.hostPlatform != stdenv.buildPlatform) [
       "--cross-prefix=${stdenv.cc.targetPrefix}"
       "--enable-cross-compile"
-      "--pkg-config=pkg-config" # Override ffmpeg's ./configure assumption that pkg-config is prefixed by the architecture. (e.g. aarch64-unknown-linux-gnu-pkg-config)
   ] ++ optional stdenv.cc.isClang "--cc=clang");
 
   depsBuildBuild = [ buildPackages.stdenv.cc ];
diff --git a/pkgs/development/libraries/gtkd/default.nix b/pkgs/development/libraries/gtkd/default.nix
index a03dc51f00c..5cef820db14 100644
--- a/pkgs/development/libraries/gtkd/default.nix
+++ b/pkgs/development/libraries/gtkd/default.nix
@@ -117,7 +117,7 @@ in stdenv.mkDerivation rec {
 
   makeFlags  = [
     "prefix=${placeholder "out"}"
-    "PKG_CONFIG=${pkgconfig}/bin/pkg-config"
+    "PKG_CONFIG=${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config"
   ];
 
   # The .pc files does not declare an `includedir=`, so the multiple
diff --git a/pkgs/development/python-modules/pkgconfig/default.nix b/pkgs/development/python-modules/pkgconfig/default.nix
index c338f6d47e5..ff9e3cc39aa 100644
--- a/pkgs/development/python-modules/pkgconfig/default.nix
+++ b/pkgs/development/python-modules/pkgconfig/default.nix
@@ -21,7 +21,7 @@ buildPythonPackage rec {
 
   patches = [ ./executable.patch ];
   postPatch = ''
-    substituteInPlace pkgconfig/pkgconfig.py --replace 'PKG_CONFIG_EXE = "pkg-config"' 'PKG_CONFIG_EXE = "${pkgconfig}/bin/pkg-config"'
+    substituteInPlace pkgconfig/pkgconfig.py --replace 'PKG_CONFIG_EXE = "pkg-config"' 'PKG_CONFIG_EXE = "${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config"'
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/zstd/default.nix b/pkgs/development/python-modules/zstd/default.nix
index 75856a88b7e..c96e08ccb51 100644
--- a/pkgs/development/python-modules/zstd/default.nix
+++ b/pkgs/development/python-modules/zstd/default.nix
@@ -12,7 +12,7 @@ buildPythonPackage rec {
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace "/usr/bin/pkg-config" "${pkgconfig}/bin/pkg-config"
+      --replace "/usr/bin/pkg-config" "${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config"
   '';
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/os-specific/linux/batman-adv/alfred.nix b/pkgs/os-specific/linux/batman-adv/alfred.nix
index c1fb3ef5ee1..04217b8989b 100644
--- a/pkgs/os-specific/linux/batman-adv/alfred.nix
+++ b/pkgs/os-specific/linux/batman-adv/alfred.nix
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ gpsd libcap libnl ];
 
   preBuild = ''
-    makeFlags="PREFIX=$out PKG_CONFIG=${pkgconfig}/bin/pkg-config"
+    makeFlags="PREFIX=$out PKG_CONFIG=${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config"
   '';
 
   meta = {
diff --git a/pkgs/os-specific/linux/batman-adv/batctl.nix b/pkgs/os-specific/linux/batman-adv/batctl.nix
index 5767c4aa72c..3b1cf183e08 100644
--- a/pkgs/os-specific/linux/batman-adv/batctl.nix
+++ b/pkgs/os-specific/linux/batman-adv/batctl.nix
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ libnl ];
 
   preBuild = ''
-    makeFlags="PREFIX=$out PKG_CONFIG=${pkgconfig}/bin/pkg-config"
+    makeFlags="PREFIX=$out PKG_CONFIG=${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config"
   '';
 
   meta = {
diff --git a/pkgs/tools/networking/openconnect_pa/default.nix b/pkgs/tools/networking/openconnect_pa/default.nix
index 2c452847aa3..4b108dc303e 100644
--- a/pkgs/tools/networking/openconnect_pa/default.nix
+++ b/pkgs/tools/networking/openconnect_pa/default.nix
@@ -16,7 +16,7 @@ stdenv.mkDerivation {
   };
 
   preConfigure = ''
-      export PKG_CONFIG=${pkgconfig}/bin/pkg-config
+      export PKG_CONFIG=${pkgconfig}/bin/${pkgconfig.targetPrefix}pkg-config
       export LIBXML2_CFLAGS="-I ${libxml2.dev}/include/libxml2"
       export LIBXML2_LIBS="-L${libxml2.out}/lib -lxml2"
   '';