diff --git a/BUILD/mdbci/copy_repos.sh b/BUILD/mdbci/copy_repos.sh
index 517ef82dd..fd9503c92 100755
--- a/BUILD/mdbci/copy_repos.sh
+++ b/BUILD/mdbci/copy_repos.sh
@@ -70,4 +70,7 @@ $(<${script_dir}/templates/repository-config/deb.json.template)
 fi
 cd $dir
 
+echo "cleaning ${unsorted_repo_dir}/$target/$box"
+rm -rf ${unsorted_repo_dir}/$target/$box
+
 ${mdbci_dir}/mdbci generate-product-repositories --product maxscale_ci --product-version $target
diff --git a/BUILD/mdbci/create_remote_repo.sh b/BUILD/mdbci/create_remote_repo.sh
index 335197d13..16f1e7b3b 100755
--- a/BUILD/mdbci/create_remote_repo.sh
+++ b/BUILD/mdbci/create_remote_repo.sh
@@ -34,8 +34,10 @@ if [ $? != 0 ] ; then
 	exit 1
 fi
 
-echo "cleaning ${unsorted_repo_dir}/$target/$box/"
-rm -rf ${unsorted_repo_dir}/$target/$box/*
+echo "cleaning ${unsorted_repo_dir}/$target/$box"
+rm -rf ${unsorted_repo_dir}/$target/$box
+echo "cleaning ${pre_repo_dir}/$target/$box"
+rm -rf ${pre_repo_dir}/$target/$box
 
 echo "copying repo from $box"
 mkdir -p ${unsorted_repo_dir}/$target/$box