Certainly, as a place of Jewish worship, it already existed when Cagliari, conquered by the Catalan Aragonese, became the capital of the Kingdom of Sardinia in 1326 and was home to a thriving Semitic community. In 1492 the Jews were expelled from all Spanish Crown States, including the Kingdom of Sardinia, and the synagogue in Cagliari was first sealed and then immediately re-established as a Catholic church dedicated to the Holy Cross. From the 16th century it was officiated by the Society of Jesus, the religious order founded in 1534 by St. Ignatius of Loyola.
The simple building was enlarged during the 17th century to a design by architect Giandomenico da Verdina. It was completed in 1661 thanks to the generosity of the Brondo family, marquises of Villacidro, as shown by the inscription on the facade under the family’s heraldic shield. Fifty-three years after the Kingdom of Sardinia passed to the House of Savoy, in 1773 the Jesuits were dissolved by Pope Clement XIV, and the church passed into the hands of the state until King Victor Emmanuel I assigned it to the Chivalric Order of Saints Maurice and Lazarus in 1809, causing it to be elevated to the rank of a magistral basilica.
In 2004, the Mauritian Order Foundation was established, which recently entrusted the basilica to the Archdiocese of Cagliari so that it could be officiated again after years of restoration.
In 2018, the Archbishop of Cagliari, in application of the provisions of Pope Benedict XVI issued with the motu proprio Summorum Pontificum on July 7, 2007, established the Parish of Santa Croce, identifying the Basilica Santa Croce as the seat for it: since this date the basilica has been officiated with the Roman rite usus antiquior (i.e., in the oldest form).