diff --git a/.github/workflows/update-subtree.yml b/.github/workflows/update-subtree.yml
index e3c07a240d7f5..94a4f4b5327eb 100644
--- a/.github/workflows/update-subtree.yml
+++ b/.github/workflows/update-subtree.yml
@@ -117,6 +117,10 @@ jobs:
         git remote add rust-filtered ../rust-tmp/
         git fetch rust-filtered
         git checkout -b subtree/library rust-filtered/subtree/library
+        # The checkout still leaves behind the library folder with submodules.
+        # We need to remove this as we'd otherwise have the create-pull-request
+        # action create an extra commit.
+        rm -rf library
         SUBTREE_HEAD_MSG=$(git log --format=%s -n 1 origin/subtree/library)
         UPSTREAM_FROM=$(git log --grep="${SUBTREE_HEAD_MSG}" -n 1 --format=%H rust-filtered/subtree/library)
         UPSTREAM_HEAD=$(git log --format=%H -n 1 rust-filtered/subtree/library)