diff --git a/src/scripts/compute_impacted_targets.sh b/src/scripts/compute_impacted_targets.sh
index b31b2f9..01ac46e 100755
--- a/src/scripts/compute_impacted_targets.sh
+++ b/src/scripts/compute_impacted_targets.sh
@@ -63,7 +63,7 @@ if [[ -n ${VERBOSE} ]]; then
 	echo "Merge Instance Depth= ${merge_instance_depth}"
 
 	git checkout "${MERGE_INSTANCE_BRANCH}"
-	git clean -dfx -f .
+	git clean -dfx -f --exclude=".trunk" .
 	git submodule update --recursive
 	git log -n "${merge_instance_depth}" --oneline
 
@@ -72,7 +72,7 @@ if [[ -n ${VERBOSE} ]]; then
 	echo "PR Depth= ${pr_depth}"
 
 	git checkout "${PR_BRANCH_HEAD_SHA}"
-	git clean -dfx -f .
+	git clean -dfx -f --exclude=".trunk" .
 	git submodule update --recursive
 	git log -n "${pr_depth}" --oneline
 fi