A Nativity scene by the school of Filippo Lippi (by some attributed to Botticelli) and an Annunciation of 14th century Florentine school dominate the inner facade of the centre nave. Following the righthand nave, one can find three paintings by Giovan Battista Naldini (1572-77) of Stories about Christ and five funerary monuments, among them those dedicated to the Blessed Giovanni da Salerno (1304), founder of the convent, and the Blessed Villana Betti (1361), carried out by Bernardo Rossellino in 1451. The Chapel of the Pure, which leads into the Cemetery of Plaona, is situated at the end of the nave.

By crossing the transept and passing through the Sacristy, one can go back along the lefthand nave, which contains a fine pulpit carried out from a design by Brunelleschi and the splendid Trinity which Masaccio painted in 1425-27, shortly before starting work on the frescoes in the Carmine. The gigantic figures of the Holy Father and His crucified Son, united by the dove of the Holy Spirit, dominate the perfect perspective of the formal architecture (possibly also designed by Brunelleschi). The Virgin, St. John and the two members of the Lenzi family who commissioned the fresco are placed below. A sarcophagus, topped by a skeleton and the words "I was once what you are and what you are yet to be", in allusion to the transience of life on earth, is painted underneath the fresco.