diff --git a/pkgs/build-support/setup-hooks/patch-shebangs.sh b/pkgs/build-support/setup-hooks/patch-shebangs.sh
index 9a48440debec..e6872db1acd7 100644
--- a/pkgs/build-support/setup-hooks/patch-shebangs.sh
+++ b/pkgs/build-support/setup-hooks/patch-shebangs.sh
@@ -11,11 +11,12 @@ fixupOutputHooks+=(patchShebangsAuto)
 
 # Run patch shebangs on a directory or file.
 # Can take multiple paths as arguments.
-# patchShebangs [--build | --host] PATH...
+# patchShebangs [--build | --host | --update] [--] PATH...
 
 # Flags:
 # --build : Lookup commands available at build-time
 # --host  : Lookup commands available at runtime
+# --update : Update shebang paths that are in Nix store
 
 # Example use cases,
 # $ patchShebangs --host /nix/store/...-hello-1.0/bin
@@ -23,14 +24,35 @@ fixupOutputHooks+=(patchShebangsAuto)
 
 patchShebangs() {
     local pathName
+    local update
 
-    if [[ "$1" == "--host" ]]; then
-        pathName=HOST_PATH
-        shift
-    elif [[ "$1" == "--build" ]]; then
-        pathName=PATH
-        shift
-    fi
+    while [[ $# -gt 0 ]]; do
+        case "$1" in
+        --host)
+            pathName=HOST_PATH
+            shift
+            ;;
+        --build)
+            pathName=PATH
+            shift
+            ;;
+        --update)
+            update=true
+            shift
+            ;;
+        --)
+            shift
+            break
+            ;;
+        -*|--*)
+            echo "Unknown option $1 supplied to patchShebangs" >&2
+            return 1
+            ;;
+        *)
+            break
+            ;;
+        esac
+    done
 
     echo "patching script interpreter paths in $@"
     local f
@@ -93,7 +115,7 @@ patchShebangs() {
         newInterpreterLine="$newPath $args"
         newInterpreterLine=${newInterpreterLine%${newInterpreterLine##*[![:space:]]}}
 
-        if [[ -n "$oldPath" && "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]]; then
+        if [[ -n "$oldPath" && ( "$update" == true || "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ) ]]; then
             if [[ -n "$newPath" && "$newPath" != "$oldPath" ]]; then
                 echo "$f: interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\""
                 # escape the escape chars so that sed doesn't interpret them
diff --git a/pkgs/test/stdenv/patch-shebangs.nix b/pkgs/test/stdenv/patch-shebangs.nix
index fb52f38ecc91..888d4a53a273 100644
--- a/pkgs/test/stdenv/patch-shebangs.nix
+++ b/pkgs/test/stdenv/patch-shebangs.nix
@@ -39,6 +39,23 @@ let
       };
     };
 
+    updates-nix-store = stdenv.mkDerivation {
+      name = "updates-nix-store";
+      strictDeps = false;
+      dontUnpack = true;
+      installPhase = ''
+        mkdir -p $out/bin
+        echo "#!$NIX_STORE/path/to/bash" > $out/bin/test
+        echo "echo -n hello" >> $out/bin/test
+        chmod +x $out/bin/test
+        patchShebangs --update $out/bin/test
+        dontPatchShebangs=1
+      '';
+      passthru = {
+        assertion = "grep '^#!${stdenv.shell}' $out/bin/test > /dev/null";
+      };
+    };
+
     split-string = stdenv.mkDerivation {
       name = "split-string";
       strictDeps = false;
@@ -59,7 +76,7 @@ let
 in
 stdenv.mkDerivation {
   name = "test-patch-shebangs";
-  passthru = { inherit (tests) bad-shebang ignores-nix-store split-string; };
+  passthru = { inherit (tests) bad-shebang ignores-nix-store updates-nix-store split-string; };
   buildCommand = ''
     validate() {
       local name=$1