I've eaten here twice, and once in the other one, at Margaretenstraße. Two times the server asked if I were celiac or just avoiding GF. When I said, I was gluten intolerant, they said that they'll prepare the bagel separately to avoid contamination. The third time, I was told, this was only possible for certain bagels. Anyway, they seem aware of the issue and take care. I was fine every time.
This place can get crowded around breakfast time, and they take no reservations. Make sure you have a plan B in case you don't get a table.
Update: the fifth time or so, I was again asked if the bagel should be prepared separately. I said, yes. I had a reaction so it was obviously contaminated.
— Somewhat
— Gluten-free items are marked on the main menu
— Some
— Good