diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index df545790f7ce0d963af398a33c0816ae535e6dab..16a078b8c9e79dbb71bd2e22b27d2db7f160417d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -306,10 +306,9 @@ setup-openappstack:
     # Set up cluster
     # TODO: I set --no-install-openappstack to skip the old installation procedure, should be removed eventually
     - python3 -m openappstack $HOSTNAME install --install-kubernetes --no-install-openappstack
-    # export IP_ADDRESS and FQDN vars
-    - source clusters/${CI_COMMIT_REF_SLUG}/.cluster.env
-    - sed "s/1.2.3.4/$IP_ADDRESS/; s/example.org/$FQDN/; s/acme_staging=false/acme_staging=true/; s/acme-staging/acme/" install/.env.example >> clusters/${CI_COMMIT_REF_SLUG}/.cluster.env
-    - source clusters/${CI_COMMIT_REF_SLUG}/.cluster.env
+    # Customize env file, remove all comments and empty lines
+    - sed "s/1.2.3.4/$IP_ADDRESS/; s/example.org/$FQDN/; s/acme_staging=false/acme_staging=true/; s/acme-staging/acme/; /^\s*#.*$/d; /^\s*$/d" install/.env.example >> clusters/${CI_COMMIT_REF_SLUG}/.flux.env
+    - set -o allexport; source clusters/${CI_COMMIT_REF_SLUG}/.flux.env; set +o allexport
     - bash ./install/install-openappstack.sh
     # TODO: Should also be removed or made up-to-date
     # Show versions of installed apps/binaries