In the only official East German championship, the 1990-91 season, the team finished last.

In 1991 the football department joined SV Fortuna Magdeburg, but in the next few years the team's performance was inconsistent.

One year later, Magdeburg narrowly missed out on qualifying for the newly created 2nd Bundesliga, finishing 6th in the Regionalliga.

In the DFB-Pokal the team reached the 2nd round for the first time in its history, losing 0–6 to Bundesliga side FFC Heike Rheine.

FC Union Berlin and SV Blau-Weiß Hohen Neuendorf, but as Magdeburg had not applied for a license for the 2nd Bundesliga, winning the championship would not have meant promotion.