diff --git a/pkgs/stdenv/generic/setup-new-2.sh b/pkgs/stdenv/generic/setup-new-2.sh
index 0dc6de22ba1..82b38c6239d 100644
--- a/pkgs/stdenv/generic/setup-new-2.sh
+++ b/pkgs/stdenv/generic/setup-new-2.sh
@@ -595,7 +595,7 @@ configureW() {
     fi
 
     if test -z "$dontAddPrefix"; then
-        configureFlags="--prefix=$prefix $configureFlags"
+        configureFlags="${prefixKey:---prefix=}$prefix $configureFlags"
     fi
 
     echo "configure flags: $configureFlags ${configureFlagsArray[@]}"