The complex of Santa Margherita degli Eremitani includes the church and the former convent. The former, built between 1282 and the 14th century, has a single nave with lateral apse chapels. Tomaso da Modena likely frescoed the Cycle of the Stories of Saint Ursula between 1355 and 1358, a masterpiece of Italian painting from the 14th century. In the cloister, in 1364, the tomb of Pietro Alighieri, son of Dante, was placed. This was deeply damaged with the arrival of Napoleon's troops at the end of the 18th century, which led the complex, particularly the church, to ruin and subsequent desecration. Fortunately, in 1883, Abbot Bailo discovered the frescoes by Tomaso da Modena; he managed to detach them from the walls and transfer them to frames that he positioned in the Church of Santa Caterina, now the "Frescoes Section" of the eponymous museum.
Severe damage was caused especially to the former convent by the air bombing of 1944; decades of abandonment followed, until the restoration in the 1980s and 1990s.