According to Calvi (1676), the large church annexed to the monastic complex of the Eremitani di S. Agostino was founded in 1290 by the will of Bishop Roberto Bonghi and consecrated in 1347 by Bishop Bernardo Bernardi.
The presence of a sepulcher bearing the date of 1315, between the side door of the church and the sacristy, testifies that it was already used for worship in that year.
Richly decorated with frescoes from the last decade of the thirteenth century, the building was only marginally affected by the great fire of 1403, in which the monastery that developed in the area north of the church was destroyed.
In 1442 the Augustinians took over from the Minori Osservanti, who promoted a vast renovation of the buildings of the convent, in which one can still see, next to fourteenth-century parts (for example the three-light windows and the portal of the ancient chapter house), other parts of the late fifteenth century ( like the first porticoed courtyard).
Following the suppression of religious orders, in the nineteenth century the church and convent were used as barracks and weapons depot; the frescoes were then hidden behind brick plasters, removed only in the 1950s and 1960s as part of the restorations directed by Mauro Pelliccioli.
Today deconsecrated, after careful conservative restoration still in progress, the building has become the seat of the University of Bergamo.