The nondenominational Christian group, which gives away groceries and hot meals to the homeless and poor, is now at the center of an arson investigation.
Director and founder Rev. Diane Dunne told Newsday that it is believed the fire was started inside the building after rear windows were shattered.
No injuries were reported, though damage was apparently severe in the area where the charity keeps its donated items.
"With Christmas and Thanksgiving right upon us, I don't know what we're going to do," Dunne told the newspaper. "It's like I'm in a bad dream."
No arrests have been made.