Mentioned for the first time in a document from 1233, the church was rebuilt starting from 1261 by will of archbishop Federico Visconti.
The church was under the patronage of the Pisane noble families, who owned a series of private chapels for their burials; the Franciscan were limited to the administration of the cult.
The works, directed by Giovanni di Simone, ended in 1270 and included also the slender bell tower.
The interior was revamped in the same age, with paintings by Jacopo da Empoli, Domenico Passignano and Santi di Tito.
The church was once home to Giotto's Stigmata of St. Francis and Cimabue's Maestà, both robbed by the French in the 1810s and now housed at the Louvre Museum.