diff --git a/pkgs/development/tools/build-managers/waf/setup-hook.sh b/pkgs/development/tools/build-managers/waf/setup-hook.sh
index 34d2ca6a3641..2593b0a9d808 100644
--- a/pkgs/development/tools/build-managers/waf/setup-hook.sh
+++ b/pkgs/development/tools/build-managers/waf/setup-hook.sh
@@ -18,7 +18,7 @@ wafConfigurePhase() {
 
     local flagsArray=(
         $prefixFlag
-        $configureFlags "${configureFlagsArray[@]}"
+        $wafConfigureFlags "${wafConfigureFlagsArray[@]}"
         ${configureTargets:-configure}
     )