Pomezania Malbork was created on 23 July 1990 after the initiative of Siegfried Kruczkowski and other local football enthusiasts with the team taking the place of MMKS ″Nogat″ in the league.

After a series of manager sackings and disappointing results Pomezania failed to capitalise on their strong start in the II liga and were relegated to the third division at the end of the 1995–96 season.

After the reorganization of the leagues' structure the team found themselves in the fourth tier, finishing third in their groups in both 2001–02 and 2002–03.

[3] In the early years the Pomezania home kit was yellow shirts, black shorts, and white socks.

The team played in the second division until the Polski Cukier sponsor withdrew from Pomezania, leading the club to fold shortly after.