diff --git a/scripts/deploy-prod.sh b/scripts/deploy-prod.sh
index cdd2d62..c927254 100644
--- a/scripts/deploy-prod.sh
+++ b/scripts/deploy-prod.sh
@@ -93,6 +93,8 @@ eval "$SSH 'mkdir -p $TARGET_DIR/data/state $TARGET_DIR/knowledge'"
 eval "$SCP '$TMP_ARCHIVE' $SSH_USER@$SSH_HOST:$TARGET_DIR/release.tar.gz"
 eval "$SCP '$TMP_ENV' $SSH_USER@$SSH_HOST:$TARGET_DIR/.env"
 eval "$SSH 'chmod 0600 $TARGET_DIR/.env'"
+# Clean the old checkout before extracting the new bundle so deleted repo files do not survive on the VPS.
+eval "$SSH 'find $TARGET_DIR -mindepth 1 -maxdepth 1 ! -name data ! -name .env ! -name release.tar.gz ! -name .deploy-revision -exec rm -rf {} +'"
 eval "$SSH 'cd $TARGET_DIR && tar -xzf release.tar.gz && rm -f release.tar.gz'"
 {
   printf '%s\n' "$BUNDLE_REV"