diff --git a/e2e/deno/cli.sh b/e2e/deno/cli.sh
index c1957a90..7d6afda7 100755
--- a/e2e/deno/cli.sh
+++ b/e2e/deno/cli.sh
@@ -66,6 +66,11 @@ case "$method" in
         ;;
     "ci")
         set -eaux
+        if [ -d .jsr-data ]; then
+            # clean up data from previous runs
+            docker compose down
+            rm -rf .jsr-data
+        fi
         mkdir .jsr-data
         ./cli.sh start
         ./cli.sh update