It had also been known as the church of San Michele degli Scalzi in Orticaia, referring to the swampy nature of the site at the time of its founding.

A church was later built at the site and was assigned to an adjacent convent of Benedictines that was established in 1178 by monks from the abbey of Santa Maria di Pulsano sul Gargano.

In the 15th century the church belonged successively to several religious orders, and before 1463 it came under the Canons Regular of the Lateran.

The interior hosts a 13th-century crucifix, painted in tempera and gilded; this artwork was originally in the church of Santi Cosma e Damiano, also in Pisa.

The organ was constructed by Anselmi-Tamburini and was brought here from the anterior parish church of San Michele in 1985.