It happened inside Alex Deli & Grocery at 1256 Flatbush Avenue, police said.
One man was shot in the face, and the other was shot in the back, officials said.
Both men were taken to the hospital in stable condition, officials said.
Police said the two men who were shot were not store employees.
Police have not said what prompted the shooting and no arrests have been made.
The United Bodegas Association condemned the violence and said it will offer a $5,000 reward for information leading to the identification and arrest of the individual or individuals responsible.
"We are sending a clear message to Mayor Mandami and Governor Hochul. We need funding for panic buttons and real security measures. Our members cannot do this alone. The City and the State must step up to protect the men and women who own and operate these bodegas," said Fernando Mateo, Spokesperson for the United Bodegas Association.