While the closing years of the 15th century saw Novacella flourishing in an era of intellectual and cultural prosperity, the 16th century ushered in a period of deep crisis for the independent monastery in the wake of social and religious upheavals. The downturn in the monastery’s fortunes began like a bolt from the blue in 1525 when, during the Tyrolean Peasants’ Revolt, marauding troops plundered the monastery complex for three days and then occupied it. Although the community disposed of sufficient economic resources to repair the physical damage to the buildings, the spiritual edifice was in grave danger of collapsing. In 1510 the chapter consisted of thirty Canons Regular, while by 1560 their number had dwindled to just six.
The tide finally began to turn under Provost Jakob Fischer (1589-1621). His successor Markus Hauser (1621-1665) founded an academic institute and in doing so laid the spiritual foundations for redesigning the monastery along baroque lines. During the 17th century the cloister and gardens were modernised and extended in order to accommodate the growing community. Later, from 1735 to 1744, the medieval collegiate church was completely rebuilt in the late baroque style to produce a ‘theatrum sacrum’ flooded with light in order to give the liturgy a foretaste of the Heavenly Banquet. The final touches were added between 1771 and 1778 with the building of the new library wing with its magnificent rococo style hall. This ambitious building work was carried out to accommodate a large community of Canons Regular who numbered 53 members in 1780.
During the French revolutionary wars there were three Coalition Wars between France, her allies and Austria (1792-1805). The monastery was used by both warring parties on numerous occasions to billet troops and was forced to pay oppressive tributes. The terms of the Treaty of Pressburg (1805) conferred the County of Tyrol including the Principalities of Brixen and Trento to the Kingdom of Bavaria. At that point the days of the Augustinian Canons Regular of Novacella seemed numbered.