In 1413 the community of nuns was disbanded, and by 1461 the Cistercian Order had redesignated the property as a monastery for monks.

In November 1568, early in the Dutch Revolt, the abbey and its church were set on fire by rebel forces.

Rebuilding began in 1589, and the church was reconsecrated in 1617 by Jean Dauvin, bishop of Namur.

The monastery was on the front lines of the War of the Spanish Succession, just a few miles from Ramillies, and suffered depredations and damage accordingly.

After the French invasion of the Southern Netherlands, the revolutionaries suppressed Boneffe Abbey along with all other religious houses.