First foundation

The abbey of Affligem was probably founded on the 28th of June, 1062 by six hermits, a group of knights who repented of their violent way of life. Hermann II, Count Palatine of Lotharingia (1061–1085) and his guardian, Anno II, archbishop of Cologne (d. 1075) are considered official founders. The count Palatine donated the land on which to build the abbey church. The first St Peterchurch was erected in 1083. The Rule of St Benedict was adopted in 1085 and the abbey was dedicated in 1086.

The counts of Brabant, also counts of Leuven, became their protectors (Vögte) in 1085/1086. A number of their family members are buried in the abbey church, including Queen Adeliza of England (d. 1151), as well as her father Duke Godfrey I of Leuven (d. 1139).

During the 12th century, the abbey became known for its strict observance of the discipline of the Cluniac reforms.

One notable monk during this period was John (Cotton?), whose treatise "de Arte Musica" (c. 1100-1121) is one of the earliest of musical theses, covering the ecclesiastical use of monody in the organum and the roots of polyphony.

Saint Bernard of Clairvaux visited Affligem in 1146, where he is said to have had a vision of the Blessed Virgin, in memory of which he gave the abbey his staff and chalice, which are still preserved in the abbey today.

Another eminent monk of this period was Jan of Afflighem, Jan van Ruusbroec's Good Cook in the Victorine monastery of Groenendaal, near Brussels, whose importance in the survival of theology in the wake of the Black Death is understated, as his theological thinking strongly influenced Gerard Groot, who taught Thomas à Kempis.

Several monasteries, among them Maria Laach Abbey in Germany, were founded by the monks of Affligem.

In 1523, Affligem joined the Bursfelde Congregation, a union of Benedictine monasteries formed in the 15th century for the stricter observance of the Benedictine rule. In 1569, the Archbishop of Mechelen became commendatory abbot and exercised his authority through a dean, an institution that lasted until the dissolution of the abbey in 1796.

Archbishop Jacob Boonen introduced the Monte Cassino observance. At his insistence, the Prior of Affligem, Benedict van Haeften, founded in 1627 a new congregation, B. M. V. in Templo Praesentat, which included Affligem and several other Belgian monasteries. It was dissolved in 1654.

In 1796, during the French occupation, the monks were dismissed, part of the buildings destroyed and the lands confiscated. The last dean, Beda Regaus, preserved the miraculous image of Our Lady, as well as the staff and chalice of Saint Bernard. These came into the possession of a Benedictine monk, Veremund Daens, who in 1838 established a new foundation at Dendermonde.

Second foundation

In 1869/70, the abbey of Affligem was re-established. It is now a member of the Flemish Province of the Subiaco Congregation within the Benedictine Confederation.