In 1500, the sculptor Giuliano Mancino was commissioned to make the marble altarpiece for the main altar, completed in 1515.
In the first decades of the 17th-century, Francesco Pellegrino (Peregrinus) painted the altarpiece depicting St Thomas verifying the Resurrected Christ.
The church has four paintings of the prophets and a Holy Family by Saverio Marchese (1806-1859), who was the brother of the priest of San Tommaso.
Based in the church is the Confraternity of the Holy Sacrament, originally established in 1687 as the Compagnia dei Bianchi, that was meant to accompany those condemned to death.
This group was dissoved in the late 19th-century during the wave of dissolutions with the advent of the Kingdom of Italy, but refounded in 1935 to as a lay Catholic organization.