In 1542 the town council introduced the Protestant Reformation and after repeated looting of the charterhouse in 1542 and 1542 the monks, under their prior Dietrich Loher (c.1495–1554), withdrew to Cologne.
When in 1543 Loher was appointed prior of Buxheim Charterhouse near Memmingen in Upper Swabia, several of the Hildesheim monks accompanied him.
Under Prince-Bishop Maximilian Henry of Bavaria the monastery was re-established inside the town walls in 1659–1660 for its better protection, between the cathedral close and the Langelinienwall.
Aly, who at his baptism took the surname "Weissenburg" after the German name of his home town, Belgrade, was still evidenced in the monastery in 1758 under his Carthusian name Pater Josephus.
The last visible structural trace of the charterhouse is the Baroque gateway in the Neue Straße, now part of the St. Bernward Hospital, with figures of the Madonna in glory, Saint John the Baptist and Saint Bruno of Cologne, the founder of the Carthusian Order, standing on pedestals above it.