diff --git a/pkgs/build-support/setup-hooks/make-wrapper.sh b/pkgs/build-support/setup-hooks/make-wrapper.sh
index 06891893e8c1..8b7012677cd5 100644
--- a/pkgs/build-support/setup-hooks/make-wrapper.sh
+++ b/pkgs/build-support/setup-hooks/make-wrapper.sh
@@ -19,9 +19,6 @@ assertExecutable() {
 #                         the environment
 # --unset       VAR     : remove VAR from the environment
 # --run         COMMAND : run command before the executable
-#                         The command can push extra flags to a magic list
-#                         variable extraFlagsArray, which are then added to
-#                         the invocation of the executable
 # --add-flags   FLAGS   : add FLAGS to invocation of executable
 
 # --prefix          ENV SEP VAL   : suffix/prefix ENV with VAL, separated by SEP
@@ -109,12 +106,8 @@ makeWrapper() {
         fi
     done
 
-    # Note: extraFlagsArray is an array containing additional flags
-    # that may be set by --run actions.
-    # Silence warning about unexpanded extraFlagsArray:
-    # shellcheck disable=SC2016
     echo exec ${argv0:+-a \"$argv0\"} \""$original"\" \
-         "$flagsBefore" '"${extraFlagsArray[@]}"' '"$@"' >> "$wrapper"
+         "$flagsBefore" '"$@"' >> "$wrapper"
 
     chmod +x "$wrapper"
 }
diff --git a/pkgs/desktops/gnustep/make/builder.sh b/pkgs/desktops/gnustep/make/builder.sh
index 1655a75eeba3..66afe1271cae 100644
--- a/pkgs/desktops/gnustep/make/builder.sh
+++ b/pkgs/desktops/gnustep/make/builder.sh
@@ -16,7 +16,7 @@ wrapGSMake() {
 
 export GNUSTEP_CONFIG_FILE="$config"
 
-exec "$wrapped" "\$@" "\${extraFlagsArray[@]}"
+exec "$wrapped" "\$@"
 EOF
     chmod +x "$program"
 }
diff --git a/pkgs/development/tools/misc/ccls/wrapper b/pkgs/development/tools/misc/ccls/wrapper
index f8d7b9eb3fea..155e6d4f6474 100644
--- a/pkgs/development/tools/misc/ccls/wrapper
+++ b/pkgs/development/tools/misc/ccls/wrapper
@@ -9,4 +9,4 @@ fi
 
 initString+="]}}"
 
-exec -a "$0" "@out@/bin/@wrapped@" "${initString}" "${extraFlagsArray[@]}" "$@"
+exec -a "$0" "@out@/bin/@wrapped@" "${initString}" "$@"
diff --git a/pkgs/development/tools/misc/cquery/wrapper b/pkgs/development/tools/misc/cquery/wrapper
index 534f900f94af..8b3e57290429 100644
--- a/pkgs/development/tools/misc/cquery/wrapper
+++ b/pkgs/development/tools/misc/cquery/wrapper
@@ -9,4 +9,4 @@ fi
 
 initString+="]}"
 
-exec -a "$0" "@out@/bin/@wrapped@" "${initString}" "${extraFlagsArray[@]}" "$@"
+exec -a "$0" "@out@/bin/@wrapped@" "${initString}" "$@"
diff --git a/pkgs/games/simutrans/default.nix b/pkgs/games/simutrans/default.nix
index d8ab792bb62a..79d7b7755da4 100644
--- a/pkgs/games/simutrans/default.nix
+++ b/pkgs/games/simutrans/default.nix
@@ -97,7 +97,7 @@ let
       cat > "$out/bin/simutrans" <<EOF
       #!${runtimeShell}
       cd "$out"/share/simutrans
-      exec "${binaries}/bin/simutrans" -use_workdir "\''${extraFlagsArray[@]}" "\$@"
+      exec "${binaries}/bin/simutrans" -use_workdir "\$@"
       EOF
       chmod +x "$out/bin/simutrans"
     '';