The works for the construction of this parish started in 1247 for the will of the Podestà of Massa Marittima and ended in 1252. At the time, this was the only church within the walls of the district of Cittanova and it was built to meet the growth of the population. The fact that it was commissioned by the Free Commune indicates the desire to assert its autonomy even in the ecclesiastical sphere.
The church had a single nave, the roof made of trusses and supporting arches and performed the functions of the Cathedral until the Cathedral of San Cerbone was built.
In 1273 the municipality ceded the church to the Augustinian friars, who created a convent, but about twenty years later transferred the parish to the brand new Church of Sant’Agostino, right next door. From the end of the 18th century until the second half of the 18th century, the building was used as a convent and later became the seat of nursery and primary schools.
Today the church of San Pietro all’Orto serves as the headquarters of the Terziere di Cittanova, while the rest of the building houses the Museum of Sacred Art, the Angiolino Martini Collection of Contemporary Art and the Museum of Ancient Mechanical Organs.