The church of Sant'Anna was consecrated in 1426 and restored by Girolamo Ammannati, together with the cloister, in the early 15th century. In 1741-47 it was completely rebuilt by the Pisan brothers Giuseppe and Francesco Melani, architects and painters.
In 1668 the complex incorporated the Church and Convent of San Girolamo dei Gesuati. The convent was suppressed in 1786, and in 1809 it was converted into a boarding school. The aisleless interior is decorated with 18th-century paintings by Tommaso Tommasi, Giuseppe Grisoni and Antonio Luchi. The convent retains traces of frescoes and a column dating from the 13th century. The cloister, formerly belonging to the Convent of San Girolamo, contains graffiti and frescoes such as ''Life of the Blessed Filippo Gambacorti'', dating from the 16th-17th centuries.
Following the fire that ravaged the cathedral in 1595, it was chosen to preserve an old wooden crucifix that was subsequently returned to the Museum of the Cathedral.