diff --git a/.github/scripts/init-repo.sh b/.github/scripts/init-repo.sh
index 99f2bcf2..47a7e971 100755
--- a/.github/scripts/init-repo.sh
+++ b/.github/scripts/init-repo.sh
@@ -263,6 +263,11 @@ license="$(config_value license 2>/dev/null || true)"
   printf 'turbo_remote: %s\n' "$turbo_remote"
 } > .github/code-foundry.yml
 
+if [ "$config_path" = .github/template.yml ] && [ -f .github/template.yml ]; then
+  rm .github/template.yml
+  printf '%s\n' 'Migrated .github/template.yml to .github/code-foundry.yml.'
+fi
+
 if [ "$bootstrap" = false ]; then
   printf '%s\n' 'Bootstrap skipped.'
   exit 0
diff --git a/.github/scripts/sync-template.sh b/.github/scripts/sync-template.sh
index 73382801..feea6540 100755
--- a/.github/scripts/sync-template.sh
+++ b/.github/scripts/sync-template.sh
@@ -702,6 +702,10 @@ if [ "$mode" = "apply" ]; then
       printf 'license_file: %s\n' "$license_file"
     fi
   } > .github/code-foundry.yml
+  if [ "$config_path" = .github/template.yml ] && [ -f .github/template.yml ]; then
+    rm .github/template.yml
+    printf '%s\n' 'Migrated .github/template.yml to .github/code-foundry.yml.'
+  fi
 fi
 
 if [ "$prune" = true ]; then