The pre-existing Roman Catholic Church dates back to the 11th century and the name (Jacopo dei Fossi=James of the Ditches TN) referred to the ditches that ran along the walls of the city. The church was Romanic and positioned differently compared to today and included a complex where the Vallombrosa Benedictine monks lives. In the Sixteenth century the Church and the convent were passed to the Augustinian monks of the Lombardy Congregation.

The current layout, with a single space (nave and aisles) and side alters dates back to the Seventeenth century renovation. After the convent was closed in 1808 and the church was deconsecrated in 1849, the space was used as a military deposit. The wooden ceiling and the Alessandro Ghilardini’s polygonal painting (c. 1690) are all that is left of the works of art once contained in the church. For a while the complex housed a Roman Catholic orphanage then, in 1874, it was purchased by Pastor John Mac Dougall, the treasurer of the Free Church of Scotland and gifted to the Chiesa Libera Italiana (Free Italian Church) run by Alessandro Gavazzi, a former Catholic priest.

This was the time when the building housed the Istituto Evangelico Ferretti (the Ferretti Evangelical Institute).  In 1905 it passed to the Wesleyan Methodist Church that in 1946 joined with the Episcopalian Methodist Church to form the Evangelical Methodist Church of Italy. The building in via de’ Benci also housed the Enrico Pestalozzi Orphanage which in 1943 merged with the Gould Institute, and moved to via de' Serragli.

Currently the Methodist Church worships with the Waldensian Church in Florence.