diff --git a/bin/BuildPackages.sh b/bin/BuildPackages.sh
index 6c60cecee6..d0121c2f66 100755
--- a/bin/BuildPackages.sh
+++ b/bin/BuildPackages.sh
@@ -168,8 +168,11 @@ run_configure_and_make() {
     if grep Autoconf ./configure > /dev/null
     then
       echo_run ./configure --with-gaproot="$GAPROOT" $CONFIGFLAGS
+      echo_run "$MAKE" clean
     else
       echo_run ./configure "$GAPROOT"
+      echo_run "$MAKE" clean
+      echo_run ./configure "$GAPROOT"
     fi
     echo_run "$MAKE"
   else