It is difficult reconstructing the architectural phases of the building due to the scarcity of sources and documents attributable to it with certainty. Of some importance are some seventeenth century drawings belonging to the Defensio Sanctitatis Beati Luciferi that scholars used to formulate several constructive hypothesis. According to the captions, the drawings depict a church dedicated to Saint Lucifer, which today disappeared. One of these drawings given the similarities with the real architecture, it has been interpreted as depicting the church of Saint Lussorio at Selargius. In the later years, the nave is strangely decentralized from the main entrance and in the attempt to explain this in particular, several hypotheses have been formulated. According to one hypothesis, the church was originally with three naves. A proof of this would be the direct testimony of the picapedrers (expert stonemasons) who worked on the restoration in 1600 at the behest of the Cagliari archbishop D’Esquivel. Following these works, the church became with a single nave.

According to another hypothesis, the church would originally be with two naves, perhaps by the monks of Saint Victor of Marseille, who had the intention of a future expansion that never happened.