Yes, the secrecy of the ballot is protected in online elections with POLYAS.
After logging into the online voting system, an anonymous token is generated by your access data. As you cast your vote using this token, your identifying access data won't be transferred with it to the digital ballot box. After casting your vote, your token will be deleted and the electoral roll will be notified that no new token can be generated for this access data.
That's how the electoral roll knows that you took part in the election without knowing how you voted. The digital ballot box knows that the ballot paper has been filled out but cannot know who filled it out. The only person who knows how you voted is you, ensuring the secrecy of the ballot is maintained.