Following the merger in 1999, the club moved from the Veltwijckstadion in the municipality of Ekeren to the Olympisch Stadion in the Kiel neighbourhood in Antwerp.

The name change was the result of an internal struggle which split the board of directors which ended with the former Germinal Ekeren board members vacating their position, giving a free path to remove the mention of Germinal[1] in the team's name by the new directors as part of a business plan to restore the former K. Beerschot V.A.C.

In addition, the club set its motto to the Latin phrase 'Tene Quod Bene', which translates as 'keep what is good', again referring to the fact that only the "Beerschot" part was kept.

[2] The youth academy of Beerschot produced the likes of Thomas Vermaelen, Mousa Dembélé, Radja Nainggolan, Jan Vertonghen, and Toby Alderweireld.

Several years earlier, in 1899, Beerschot was founded at Het Kiel, a southern outskirt of Antwerp, where the 1920 Olympics had been held.

However, in 1999, due to the low attendance of supporters and limited expansion possibilities in Ekeren, the club merged with Beerschot who were then playing in the 3rd division and themselves had severe financial problems.

By keeping the matricule of Ekeren, the honours of Beerschot were considered to be distinct and separate from the new team and the club finally dropped the name Antwerpen in 2003.

After only 7 matches in the Jupiler League 2005-06 season, he was fired due to bad results (4 points from 21 and a 3–0 defeat against the 18th placed team).

After having failed to present a financial plan to the Royal Belgian Football Association, the club had lost its license to play in the 1st division.

In the 2008 Intertoto Cup, they met Neftchi Baku of Azerbaijan in the second round, drawing 1–1 at home but losing 0–1 away to be eliminated from the competition.