The 32 year old died in hospital two hours after being shot, police report.
Witnesses had alerted cops after hearing shots fired in an alleyway off Kottbusser Tor at around 10pm. They also saw a man running from the scene.
The witnesses then found the victim with bullet wounds to his upper body.
Police say that the background to the incident is still unclear.
But local media are reporting that the man was the victim of a biker war over control of the junction, which is well known as one of the centre points for the drug trade in the capital city.
Tabloid BZ reports that police suspect at least two men were involved in the murder and that they were members of the Hells Angels, who control some of the drug dealing in the area. The newspaper has published photos of two Harley-Davidson motorbikes which were parked in the vicinity of the murder scene.
The victim, who had a wife and two children, was once a member of a rival gang and had been attempting to mediate with the bikers after they had made threats, the tabloid reports.
A resident, who claimed to be related to the victim by marriage, also told Tagesspiegel that the “he wanted to negotiate, but ended up stuck between two fronts.”
Kottbusser Tor, known locally as Kotti, in Kreuzberg has been synonymous with crime for years.
However, recently recorded criminality has risen sharply. In the first half of 2016 there were 52 reported robberies in comparison with 83 in the whole of 2015, 49 cases of physical assault compared to 67 for the whole of 2015, and 32 cases of resistance against police as opposed to 27 in 2015, BZ reports.