The original design called for a single nave with large transepts and several side chapels, but the building was refurbished in starting in the early 17th century, to a more grandiose layout typical of Jesuit architecture.

In 1892, cavaliere Salvatore Di Pietro, philanthropist, former rector of the Casa Professa, prefect of studies at the seminary, and member of the Theological College, of the Academy of Sciences, letters and arts and of the Accademia di storia patria, convinced in 1888 the minister of public education, Paolo Boselli, to decree the church a national monument.

These frescoes were replaced during two years' restoration work, after which the church reopened on 24 February 2009 with a solemn mass presided over by Paolo Romeo, archbishop of Palermo, and attended by several Jesuits and civil and military officials.

In the lower part there are three portals, above are niches with statues of St Ignatius of Loyola, a Madonna with Child and Francis Xavier.

Masucci originally planned belfries, but these were not completed, and the current 18th-century campanile was built on the adjacent Palazzo Marchesi.