diff --git a/run-eclair-builds.sh b/run-eclair-builds.sh
index 202e469..3ed9e7f 100755
--- a/run-eclair-builds.sh
+++ b/run-eclair-builds.sh
@@ -16,9 +16,9 @@
 for cfg in $(python3 ./tf-m-ci-scripts/configs.py -g "$FILTER_GROUP"); do
     echo "============== $cfg ($cnt/$num_configs) =============="
     export CONFIG_NAME=$cfg
-    (cd mbedtls; git checkout .; git clean -fq)
-    (cd psa-arch-tests; git checkout .; git clean -fq)
-    (cd trusted-firmware-m; git checkout .; git clean -fq)
+    (cd mbedtls; git checkout-index -faq; git clean -fdq)
+    (cd psa-arch-tests; git checkout-index -faq; git clean -fdq)
+    (cd trusted-firmware-m; git checkout-index -faq; git clean -fdq)
     eclair_tfm_set_toolchain_path
     detachLicense $LICENSE_LEASE
     tf-m-ci-scripts/run-build.sh