Police say 19-year-old Amir Alawadi struck 55-year-old Hisham Zidan across the head with a metal object, killing him.
Zidan, who had a family of eight children in Jordan, was found in the basement of the deli in East New York last Friday morning.
Cash, cigarettes and lottery tickets were also stolen.
Zidan's friends say he knew the dangers of working alone in a corner store during late night hours in a not-so-friendly neighborhood and that robbery was always a risk.
"It happened to him before," coworker Abdullah Mohamed said. "He got robbed one time, but he told them take the money, just save my life."
A customer called 911 around 5 a.m. after walking into the store and seeing the register on the floor.
Officers found Zidan in the basement with a fatal head injury.
"They took a metal piece, I don't know," Mohamed said. "They just smacked him with it."
Mohamed believes the robbers broke in through a back door and waited for Zidan in the basement, where he would often go to use the bathroom.