After the edifice was partially destroyed by a fire after the Allied bombings during World War II, it was brought back to the alleged original state by a disputed restoration, which was completed in 1953.

An unusual feature of the building is that the lateral chapels are absorbed into the body of the church, giving Santa Chiara its distinctive rectangular appearance.

The nuns choir is different in plan from the main body of the church, with two large piers supported by rib vaults dividing the space into three sections.

[2] In the side chapels are the tombs of the Bourbon king of Naples, Francis II and his consort Maria Sophie of Bavaria, as well as those of Queen Maria Christina of Savoy and of the national hero Salvo D'Acquisto (a carabiniere who sacrificed his life to save the lives of 22 civilian hostages during the Nazi occupation).

The church was used, even before it was formally completed, to hold the relics of Saint Louis of Toulouse, elder brother of King Robert.

One of these relics was the brain of St. Louis, in an ornate reliquary decorated with a crown Queen Sancha had donated in memory of her brother-in-law.

In the sixth chapel to the left, are 14th-century bas reliefs depicting the Martyrdom of the wife of Massenzio, while the seventh has a tomb of Louis, a son of Charles, Duke of Durazzo, another 14th-century work by the Florentine Pacio Bertini.

The cloister of the Clarisses is known for the unique addition of majolica tiles, added in 1742 by Domenico Antonio Vaccaro in Rococò style.