During the first half of the 16th century, the church was remodelled at the request of Andrea Doria and took on a more gothic appearance, with only the front surviving through to the present day. A mosaic representing St Matthew was added to the entrance, and a Roman sarcophagus, a trophy from the battle of Curzola against the Venetians, was installed at the base of the right window.

The tomb of Andrea Doria was placed in the crypt inside the church.