Thanks. As far as I know, after the zip deployment the web app is going to restart. You can try to use the lightweight API to use the Azure-CLI as a tool and invoke commands like az webapp deployment source config-zip --resource-group <RESOURCE GROUP> --name <WEB APP NAME> --src <ZIP FILE PATH> (you are going to need to run az login prior that). About the secrets, you are right environment variables in the CI server are how I deal with that.