Renovated as early as the second half of the 13th century, it was extended in 1367 in the eastern part, obtaining its current rectangular plan.

In 1471, a first loggia was built above the church and, probably, the circular tower to the left of the current entrance. During the 16th century, other open galleries were built, the same ones that can still be seen on three sides of the inner courtyard, incorporating parts of the 15th-century ones. It was probably on the occasion of these new works, or shortly before them, that the two frescoes depicting the Nativity and a composition with the Virgin, St. John the Baptist and St. James were painted inside the church. Further, but minor, work took place in 1644, when the sandstone puteal was built on an existing cistern.

Furthermore, in 1502, the conspiracy (diet at the Magione in Perugino) hatched by some nobles against Cesare Borgia, ‘ about which Macchiavelli speaks in “The Prince”, was held here. 

The name Badia, used by the Magione inhabitants for his structure, established itself in modern times, when the term Magione was no longer indicated the castle (something that was already happening in the 16th century), but referred to the village in place of the more ancient Pian di Carpine. The documentation from the late 15th century refers to the abbatia (abbey) Mansionis Plani Carpinis.

Currently the buildings are used as the operational centre of a large farm and vineyard. Local wines were praised by the humanist Giannantonio Campano who, in the mid-15th century, stated that there were few districts producing better wines than those from around Lake Trasimeno.