At the end of the Middle Ages, the abbey went through a difficult time, when it was subjected to the fierce flames of two fires, and was pillaged several times.
In the second half of the 16th century, it began to flourish once more and pilgrims came in increasing numbers. In 1629, a large building was added to the abbey in order to accommodate guests: la maison des étrangers.
In the 18th century, Abbot de Harlez demolished the Gothic church and cloister and began the construction of a new abbey.