The convent originally included seven cloisters (the main courtyard, St. Bonaventure, St. Francis Solanus (who is buried in the monastery church), the Pepper Yard, the Infirmary, the Novitiate and the Third Order). During the works to open Abancay Avenue in the 1940s, part of the monastery (including St. Bonaventure's courtyard) was demolished, and the section used by the Franciscan Third Order was separated from the main structure.