The complex was built in 1418 with a donation made by Carlo Malatesta, ruler of Rimini from 1385 to 1429, who had a country residence in the vicinity. The church and monastery were entrusted to the Augustinians of St Paul the First Martyr of Hungary, inexplicably recalled to Hungary in 1420. Carlo then assigned the complex to the Benedictines of Mount Oliveto Maggiore, who owned the abbey and its estates until 1797, when they were expelled during the Napoleonic suppressions.
The Olivetans greatly enlarged and altered the abbey. The original church was rebuilt and enhanced with numerous works of art. The façade seen today bears the arms of Roberto Malatesta, the ruler of Rimini from 1468 to 1482, but the panelled ceiling with the arms of Carlo Malatesta at the centre is from a later date. The two side chapels, currently used as sacristies, were added in the early 1500's, and the right-hand one was frescoed by Girolamo Marchesi da Cotignola. Giorgio Vasari (1511-74), who visited the abbey to have a copy made of his “Le vite de’ più eccellenti architetti, pittori et scultori italiani, da Cimabue insino a’ tempi nostri”, painted an altarpiece for the monks in 1547-48 showing the Adoration of the Magi, which now hangs in the choir. After the order of Olivetans was suppressed, the church was given the title of the Parish Church of San Fortunato, transferred from an older church further down the hill.
The entire complex was seriously damaged in the Second World War, and has not been fully reconstructed.