The club was established in 1999 as the result of the merger between K Beerschot VAC and KFC Germinal Ekeren, from which they took over the matricule number and history. Prior to the merger, Germinal Ekeren had been a first division club for 10 years, while 7 times Belgian champion Beerschot was struggling with financial problems in the third division. The club won 2 Belgian Cups, one as Germinal Ekeren in 1997, the other as Germinal Beerschot in 2005. Their best league ranking was a 3rd place in 1995–96 and in 1997–98.