The trio burst into the EuroGarages Esso filling station, in Wetherby Road, near Seacroft, at about 9.40pm yesterday (Sunday).
It comes just four days after two masked men armed with a knife and a screwdriver targeted the same petrol station on Wednesday.
In the latest robbery, the trio threatened an employee inside, who was working alone, before assaulting him with a pen yesterday.
The victim suffered "a number of minor puncture wounds" to his arms as a result of the attack, a spokesman for West Yorkshire Police said.
He was forced to open the safe and the offenders, who had their faces covered, stole cash and scratchcards.
They also took cash from the till and cigarettes from the counter.
The trio then fled the scene in a black BMW, driven by a fourth man, which displayed cloned registration plates reading "NJ15RYB".
Detective Inspector Richard Holmes, of Leeds District CID, said: “This was obviously a very frightening experience for the victim to be confronted by these masked men and threatened and assaulted.
“We are carrying out enquiries to identify the suspects and would like to hear from anyone who witnessed the incident or saw the black BMW leaving the scene or since then. We would also like to hear from anyone with any other information that could assist the investigation."
On Wednesday, two masked men armed with a knife and a screwdriver stole money and cigarettes from the same petrol station in Wetherby Road.
Police were called at about 7.30pm after the men threatened staff and demanded cash.
No-one was injured during the robbery on Wednesday.
Det Insp Holmes said there was no evidence suggesting the two robberies were carried out by the same offenders.
He added: “We are aware that the same premises was robbed in similar circumstances on Wednesday last week but there is nothing at this stage to suggest the same suspects are responsible.”
Anyone with any information is asked to contact Leeds District CID via 101, quoting crime reference 13180642710 or call the independent charity Crimestoppers anonymously on 0800 555 111.