The church is decorated with artworks by prominent 16th- and 17th-century masters.
The first chapel on the right contains Sebastiano del Piombo's Flagellation and Transfiguration (1516–1524). Michelangelo, who had befriended Sebastiano in Rome, supplied figure drawings that were incorporated into the Flagellation.
The second chapel has a fresco by Niccolò Circignani (1654), some Renaissance frescoes from the school of Pinturicchio, and an allegorical sibyl and virtue attributed to Baldassarre Peruzzi.
The fourth chapel has a ceiling fresco by Giorgio Vasari. Although there is no grave marker, tradition has it that Beatrice Cenci—executed in 1599 for the murder of her abusive father and made famous by Percy Bysshe Shelley, among others—is buried either in this chapel or below the high altar.
The ceiling of the fifth chapel contains another fresco, the Conversion of St. Paul, by Vasari. The altarpiece is attributed to Giulio Mazzoni, while the funerary monument of Innocenzo Ciocchi Del Monte, Cardinal Giovanni Maria Del Monte and Roberto Nobili are by Bartolomeo Ammannati.