Hi @tobi,
Upgrading passbolt using docker is as easy as running the new version of the docker container.
The container runs all database migrations on boot. You just need to make sure you are mounting the serverkeys and any other directory you want to persist (i.e. images directory).
Are you using docker-compose to run passbolt?
If that is the case there is another thread on this forum about upgrading passbolt using docker and docker-compose. Keep in mind the community thread I just mentioned is to upgrade passbolt PRO edition so the docker-compose.yml file might not be exactly the same as yours.