The abbey went through a prosperous period in the first half of the 16th century, under Abbot Gerard vander Schaeft. The church was rebuilt and richly decorated. Unrest and plundering troops made it necessary to flee the abbey four times in this period. Political and religious instability in the latter half of the century, with the Beeldenstorm, made the canons flee the abbey again in 1578 to the refuge of Diest. The death of 12 monks in 1579 because of the bubonic plague reduced the abbey to only 28 monks in 1584. They returned to Averbode only in 1604.