The flames broke out inside the building on Church Avenue at East 31st Street in Flatbush just before 7 a.m.
NewsCopter 7 was over the scene as firefighters worked to secure lithium-ion batteries.
The fire is said to have damaged Lenny's Pizza on the first floor, the two floors above as well as the roof.
Two firefighters were treated for minor injuries.
A charred e-bike was recovered from the store, as well as the e-batteries. It is unknown if it played a role in the fire.
The cause of the fire remains under investigation.
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