diff --git a/system_setup/sync_client_software.sh b/system_setup/sync_client_software.sh
index ca4f685..7a44ed1 100755
--- a/system_setup/sync_client_software.sh
+++ b/system_setup/sync_client_software.sh
@@ -52,7 +52,7 @@ if [[ ! -z "${REPO_URL}" ]]; then
             # Doing upgrade, discarding all local changes frist (is more save than forced pull)
             echo "Checks have passed, we are now upgrading via git."
             #Fetch latest commit only (depth=1), reset working tree, purge old history and untracked files
-            git fetch --depth=1 origin ${REPO_BRANCH} && git reset --hard FETCH_HEAD && git clean -fd && git gc --prune=now --quiet
+            git fetch --depth=1 origin ${REPO_BRANCH} && git reset --hard FETCH_HEAD && git -C "${SYSCONFIGPATH}" clean -fd && git gc --prune=now --quiet
             if [[ $? -ne 0 ]]; then
                 echo "Error: Failure while updating, will continue as is."
             fi