The chain of Back-Factory bakery/cafes offer a very affordable option for breakfast or light lunch. They are scattered all around the town, just look up the closest location to wherever you are staying from their website.
Since our hotel breakfast was so exorbitantly priced, we opted to visit the Back-Factory in the Moabit district every morning. The place was usually pretty packed and it was a bit of squeeze to get ourselves a place to sit.
Especially the bagels were exceptionally good, and considering the price really a steal.
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