The fire broke out inside one store on Queens Boulevard around 2:14 a.m. and quickly spread.
Dozens of firefighters were called to the scene as the fire grew to five alarms.
The raging flames eventually engulfed six stores, one of which partially collapsed in the back.
Firefighters dodged a frightening backdraft that ripped through one building around 3 a.m., sending them scrambling to Queens Boulevard for safety.
Firefighters experience terrifying backdraft
One man on the scene reported seeing the fireball as firefighters attempted to get out of the building.
"I saw three firefighters just on the ground on Queens Boulevard," the witness said. "They flew out of the basement, and I saw one of the guys picked up his helmet and he ran back there to do his job. I was terrified."
Firefighters evacuated six families from a neighboring building before the blaze was declared under control. An MTA bus was brought to the scene to help shelter the displaced residents.
Of the 12 people injured, seven are firefighters and five are civilians.
Most of the injuries were described as minor, but one civilian suffered serious injuries, which were said to be fractures. He is expected to survive.
"I was heartbroken to learn of last night's devastating fire in Sunnyside impacting local businesses and neighborhood residents," Senator Michael Gianaris said in a statement. "I reached out to various agencies, including the American Red Cross, Office of Emergency Management, FDNY, Small Business Services, and the Small Business Administration to offer my assistance in recovery and rebuilding efforts. A number of firefighters and residents were injured during the incident. My thoughts are with them and their families in hopes of a speedy recovery. I thank them and the more than 200 FDNY members who responded for their bravery."
Queens Boulevard was closed from 44th to 47th streets, and the MTA Q60 bus and Q32 bus were being rerouted. An MTA supervisor was on the scene.
Number 7 subway service was not affected.
The cause of the fire is under investigation.
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