[5] The interior is on the Egyptian cross plan with a huge nave covered by trusses and with a transept featuring high chapels.
The entrance to the basilica is on the left side of the church because the area behind the façade is occupied by the raised structure of the Chapel of the Vaults.
The left wall of the nave has the famous painting Madonna with Child by Francesco di Vannuccio, framed by an Eternal with Saint by Il Sodoma and by a predella with fifteen Stories of the New Testament by Antonio Magagna.
Rutilio Manetti painted a St. Anthony Abbot's Exorcism, Sebastiano Folli a St. Catherine of Alexandria and Francesco Vanni a St. Hyacinth Saving a Statue of the Madonna from a Fire.
They are followed by the St. Catherine Chapel in Baroque style, with, in the centre, an altar housing the saint's head and thumb.
Notable amongst the chapels are the second, entitled to the martyrs of the German Nation, and the third, which includes a Madonna with Child and the Saint Jerome and John the Baptist by Matteo di Giovanni.
The altar has a ciborium with two angels by Benedetto da Maiano (1475–1480), while in the apse is a Death of St. Peter Martyr by Arcangelo Salimbeni (1579) and St. Thomas and the Pope by Galgano Perpignani.