The early Christian church of San Giovanni di Sinis stands on a cemetery area that was originally pagan and later Christian. The church is made of golden sandstone blocks and oriented with the apse to the east. The rectangular hall is divided into three naves, covered by barrel vaults and ending in a similarly vaulted transept. In the central nave and the apse, there is a small dome supported by large pillars.

The side naves communicate with the central one through three arches resting on simple pillars. The building is illuminated in the central nave by three small quadrangular openings, and by biforate windows in the apse and transept. The sober facade is enlivened in the central part by an oculus located above the entrance door.
The central core of the church, consisting of the domed area and attributable to an original Greek-cross building inscribed in a square, was probably established in the 6th century AD.
During the Sardinian Judicate era, between the 9th and 11th centuries, the structure underwent a radical transformation, adding the apse and the three-nave hall, replacing the eastern and western arms, and opening the biforate windows.

During recent restorations, a fragment of painted plaster in brown and red on a white background was found at the base of the apse, depicting part of a curtain (velarium). This element, which was part of a larger wall decoration, is similar to other archaeological contexts outside Sardinia dated between the 8th and 9th centuries.
During the same restoration work, a pre-existing building with an east-oriented apse was identified beneath and south of the church. Due to the presence of numerous burials in the area, including some sarcophagi still present beneath the floor, it is hypothesized that the identified wall remains refer to an early Christian funerary basilica.