diff --git a/vendorsetup.sh b/vendorsetup.sh
index cd134fd1e87c53b716ee4fa25d8cde28de99a693..cd2c2203124ad62a27ddb379498b7599defbcd18 100644
--- a/vendorsetup.sh
+++ b/vendorsetup.sh
@@ -101,6 +101,9 @@ __patch_tree()
                    git branch b2g_autogen_ephemeral_branch && \
                    git checkout b2g_autogen_ephemeral_branch \
                  )
+               if [[ -d .git/rebase-apply ]]; then
+                 git am --abort
+               fi
             else
                read -p "Project $1 is not managed by git. Modify anyway?  [y/N] "
                if [[ ${REPLY} != "y" ]]; then