Video from the scene on Fulton Street in Cypress Hills shows a number of plants inside a second-floor apartment.
The flames broke out just after 10:30 a.m. on the floor below.
The fire went to a second alarm, more than 100 firefighters responded to the scene.
It's unclear whether any of the equipment aiding in the growth of the plants sparked the fire.
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"The building had extensive damage to the first floor. And there was damage also inside the base cellar," FDNY Deputy Chief Fred Schaaf said.
The flames were brought under control just after 12:10 p.m.
No one was injured.
Police have taken possession of the plants.
They're now investigating alongside the fire marshall.
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