It happened just after 4 a.m. Tuesday at the Exxon on the 7100 block of Torresdale Avenue.
The entire incident was caught on surveillance camera.
Police say three masked men entered the gas station's mini-mart and broke into the employee side of the counter.
They attacked the 67-year-old store clerk and shot him once in the back.
A family spokesperson camera identified the victim as Patro Siboram. He said he leaves behind a wife and son.
"He's a very good guy, honest guy, hard worker," said Shaheed Jan.
Jan was a former manager at Exxon. He knew Siboram for 15 years.
"Need money? Take the money, but don't kill somebody," said Jan.
"You can see them physically struggle with him and that's when he gets shot," Philadelphia Police Chief Inspector Scott Small said.
Police say, after the victim collapsed, the three suspects forcibly removed the cash register and fled the store.
Officers arrived and found the clerk lying on the floor unresponsive.
The officers were removing the victim from the store to take him to the hospital when medics arrived.
They pronounced him dead at the scene.
Police say the longtime gas station clerk was familiar with the officers who patrol the area.
Action News spoke to customers who knew the clerk. One said he changed his habits because of past crimes at the gas station including carjackings.
"He won't even smoke out here. For many years he would take a cigarette break out here and he just completely stopped because he was too scared something like this would happen. We just had this conversation last week. And today, we're standing here and now he's gone. It's just really heartbreaking," a customer who did not want to be identified said.
Investigators are reviewing the store surveillance video and seeing if outside cameras recorded a getaway vehicle.
There were no injuries to any other employee or customers.
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