The end of the 13th century was also the end of the first period of prosperity of the monastery. The money economy replaced the economy in kind, wealthy families became impoverished, including the family of the founders of the monastery and families of some nuns. Property had to be sold. Only with the appeal of Bishop Henry III to support the monastery, the situation became better.

In 1350, pilgrimages to St. Mary's began to fill the coffers. In 1383, Count Gerhard von Wohldenberg died as the last male descendant of the county.

The second heyday of the monastery began in the 15th century. Both spiritually and economically, life in the monastery was driven by reform ideas. The monastery's reform efforts gained renewed popularity and led to the occupation of the abandoned Augustinian convent of Derneburg. However, repeated efforts to formally accept the monastery into the Cistercian Order were unsuccessful. The bishop in charge refused to give his consent.

In 1523, the bishop in charge, Johann IV of Hildesheim, lost the convent to Duke Heinrich II of Brunswick-Wolfenbüttel. He was a Catholic and let the nuns keep their confession. The monastery remained with its denomination even through the Protestant dominion of the country and, after the return of Duke Heinrich II, continued as a Catholic monastery until 1568.

It was not until Duke Julius, youngest son of Duke Heinrich II of Brunswick-Wolfenbüttel, that the monastery was converted into a Protestant ladies' convent. At this time, the precious illuminations and manuscripts were removed from the monastery and moved to the library in Wolfenbüttel. Unknowingly, the valuable works of art were thus protected from looting by Wallenstein's soldiers in 1625.

The monastery remained a Protestant ladies' convent until 1630. After the convent reverted to the diocese of Hildesheim in 1630, it was handed over to the Jesuit order. Since the nuns refused to leave the convent, according to tradition they were carried out of the convent by force and on chairs. Only two years later the monastery became Protestant again. The troops of the Swedish King Gustav-Adolf had ousted the Jesuits from the region. A short time later, the monastery was returned to the Principality of Hildesheim and occupied by Teistungenburg nuns.

From 1650 the monastery was under the paternity of the Abbot of Altenberg. Confessional peace returned.

In 1676 a devastating fire broke out and destroyed large parts of the monastery buildings, including partly the monastery church. Thanks to the great efforts of the abbesses, the monastery was quickly rebuilt. In the following 150 years, the nuns of the monastery were able to take care of social tasks. They helped the sick and the poor. Catholic children were also taught to read and write. This was made possible by a very good economic management of the monastery and the rich properties.

In 1809, Jérôme Bonaparte, Napoleon's brother, caused the dissolution and sale of the monastery. Jérôme was King of Westphalia at that time and had won a victory over Prussia over this territory in 1806. The monastery property went to the banker Israel Jakobson. However, the latter had to sell it on to the Hanoverian government as early as 1816. He was a Jew and not entitled to land ownership at that time.

Nine years later, the entire assets of the monastery were transferred to the newly founded Klosterkammer Hannover. It leased it out until 1929 and has since managed it itself as its official residence.

Wöltingerode as a rural women's school existed from 1918. For economic reasons, the rural women's school gave up the monastery property in 1990.

Until 1994, the convent building of the monastery estate was used by the Christliches Jugenddorfwerk Deutschlands e. V. (Christian Youth Village Association of Germany).

After that, the Welfenakademie (Guelph Academy) was located on the premises as a vocational academy for dual business studies.

Since 2007, the former convent building was then redesigned as a hotel and since then has been continuously developed into what it is today.