diff --git a/pkgs/development/tools/continuous-integration/github-runner/default.nix b/pkgs/development/tools/continuous-integration/github-runner/default.nix
index aa1941fa3d19..ff47eeb72b2c 100644
--- a/pkgs/development/tools/continuous-integration/github-runner/default.nix
+++ b/pkgs/development/tools/continuous-integration/github-runner/default.nix
@@ -225,15 +225,21 @@ stdenv.mkDerivation rec {
 
     # Install the helper scripts to bin/ to resemble the upstream package
     mkdir -p $out/bin
-    install -m755 src/Misc/layoutbin/runsvc.sh        $out/bin/
-    install -m755 src/Misc/layoutbin/RunnerService.js $out/lib/
-    install -m755 src/Misc/layoutroot/run.sh          $out/lib/
-    install -m755 src/Misc/layoutroot/config.sh       $out/lib/
-    install -m755 src/Misc/layoutroot/env.sh          $out/lib/
+    install -m755 src/Misc/layoutbin/runsvc.sh                 $out/bin/
+    install -m755 src/Misc/layoutbin/RunnerService.js          $out/lib/
+    install -m755 src/Misc/layoutroot/run.sh                   $out/lib/
+    install -m755 src/Misc/layoutroot/run-helper.sh.template   $out/lib/run-helper.sh
+    install -m755 src/Misc/layoutroot/config.sh                $out/lib/
+    install -m755 src/Misc/layoutroot/env.sh                   $out/lib/
 
     # Rewrite reference in helper scripts from bin/ to lib/
-    substituteInPlace $out/lib/run.sh    --replace '"$DIR"/bin' "$out/lib"
-    substituteInPlace $out/lib/config.sh --replace './bin' "$out/lib"
+    substituteInPlace $out/lib/run.sh    --replace '"$DIR"/bin' '"$DIR"/lib'
+    substituteInPlace $out/lib/config.sh --replace './bin' $out'/lib' \
+      --replace 'source ./env.sh' $out/bin/env.sh
+
+    # Remove uneeded copy for run-helper template
+    substituteInPlace $out/lib/run.sh --replace 'cp -f "$DIR"/run-helper.sh.template "$DIR"/run-helper.sh' ' '
+    substituteInPlace $out/lib/run-helper.sh --replace '"$DIR"/bin/' '"$DIR"/'
 
     # Make paths absolute
     substituteInPlace $out/bin/runsvc.sh \
@@ -269,7 +275,7 @@ stdenv.mkDerivation rec {
     wrap() {
       makeWrapper $out/lib/$1 $out/bin/$1 \
         --prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath (buildInputs ++ [ openssl ])} \
-        ''${@:2}
+        "''${@:2}"
     }
 
     fix_rpath Runner.Listener
@@ -279,10 +285,13 @@ stdenv.mkDerivation rec {
     wrap Runner.Listener
     wrap Runner.PluginHost
     wrap Runner.Worker
-    wrap run.sh
-    wrap env.sh
+    wrap run.sh --run 'export RUNNER_ROOT=''${RUNNER_ROOT:-$HOME/.github-runner}'
+    wrap env.sh --run 'cd $RUNNER_ROOT'
 
-    wrap config.sh --prefix PATH : ${lib.makeBinPath [ glibc.bin ]}
+    wrap config.sh --run 'export RUNNER_ROOT=''${RUNNER_ROOT:-$HOME/.github-runner}' \
+      --run 'mkdir -p $RUNNER_ROOT' \
+      --prefix PATH : ${lib.makeBinPath [ glibc.bin ]} \
+      --chdir $out
   '';
 
   # Script to create deps.nix file for dotnet dependencies. Run it with