The building had been changed without planning consent and began operating without permission as a shisa bar, restaurant and a takeaway.
An enforcement notice was served in 2018.
But this, along with two visits by officers who seized pipes and tobacco, was ignored, and the rules were still being broken four years later, the court heard.
The cafe has since shut down but residents on Wilmslow Road had to deal with the impact of the illegal operation for years, the court heard.
Manchester City councillor Gavin White said the operators “turned a blind eye to the law”, adding that running an illegal shisha cafe was “not a victimless crime”.
Customers were put at risk, and residents had to “put up” with the operation for “far too long”, he added.
The confiscation orders should show “we will not tolerate businesses who have no regard for the law”, Mr White said.
