Since the start of the 17th-century the church was assigned to the Franciscan order, who built an adjacent convent. It stood surrounded on three sides by the 16th-century city walls. In 1818, an earthquake caused the roof to collapse. The small church present now was rebuilt after the 1693 earthquake, with traces of the ancient Roman substructures in the crypt. The church houses the putative sarcophagus of Saint Agatha with Roman marble and Byzantine stone additions. Now used as an altar, it once housed the relics of the saint.