diff --git a/pkgs/build-support/setup-hooks/prune-libtool-files.sh b/pkgs/build-support/setup-hooks/prune-libtool-files.sh
index 2413624124f..5d7432e8f09 100644
--- a/pkgs/build-support/setup-hooks/prune-libtool-files.sh
+++ b/pkgs/build-support/setup-hooks/prune-libtool-files.sh
@@ -8,7 +8,7 @@
 fixupOutputHooks+=(_pruneLibtoolFiles)
 
 _pruneLibtoolFiles() {
-    if [ "$dontPruneLibtoolFiles" ]; then
+    if [ "$dontPruneLibtoolFiles" ] || [ ! -e "$prefix" ]; then
        return
     fi