diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d8f1f7b3d9..2fd8d9ae81 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -166,6 +166,8 @@ checkupdates_runner:
     - echo "${CHECKUPDATES_SSH_DEPLOY_KEY}" | tr -d '\r' | ssh-add -
     - url_host=$(echo "${CI_REPOSITORY_URL}" | sed -e 's|https\?://gitlab-ci-token:.*@|ssh://git@|g')
     - git remote set-url --push origin "${url_host}"
+    - git rebase --abort
+    - rm -fr ".git/rebase-apply"
   script:
     - fdroid checkupdates --allow-dirty --auto --commit ${CHECKUPDATES_APPIDS} 2>&1 | tee /tmp/out || true
     - git pull --rebase origin master