At the beginning of the 18th century, the Order of the Blessed Virgin Mary of Mercy (Mercedarian Friars) conceived of a great basilica in honour of Our Lady of Bonaria. The new church would, it was planned at the time, contain the original 13th-century Sanctuary of Our Lady of Bonaria inside, as a chapel. This original Sanctuary currently exists as a separate building standing beside the Basilica.
Work began in the basilica in 1704. After a number of different interventions and long pauses between one century and another, was it finally completed in 1960. The original planner for the project was Antonio Felice De Vincenti, a military engineer who designed it in the Piedmontese baroque style. He also had a wooden model of the Basilica project constructed. The work was unable to continue, though, for lack of funds. After several interruptions, they began again towards the end of 18th century, this time entrusting the task to the tutelage of De Vincenti's pupil Giuseppe Viana, also a military engineer. The new supervisor was not keen on his master's plan, however: the idea of the great baroque Basilica was, therefore, abandoned for a more sobre classical construction.
The basilica was inaugurated and opened for worship at the beginning of the second half of the 20th century. It suffered serious damage in 1943 during the allied bombardments which struck Cagliari. The bombs caused irreparable damage: the frescoes were completely destroyed, as were a large number of other treasures. In the post-war period, the patient and slow task of reconstruction began, which only ended in 1998, for Easter. Vitally important to the success of the restoration was the contribution of Cagliari City Council. Inside the Basilica, near the entrance door, a series of texts and photos document the history of the church, showing how it looked before and after the restructuring.