Cesari's first major work, done in his twenties, was the painting of the right counterfacade of San Lorenzo in Damaso, completed from 1588 to 1589.

On 28 June 1589, he received the commission for the murals of the choir vault in the Certosa di San Martino in Naples.

From 1591 he was again in Rome, where he painted the vault in the Contarelli Chapel within the church of San Luigi dei Francesi.

He also completed murals in the Cappella Olgiati in Santa Prassede, and the vault of the Sacristy in the Certosa di San Martino.

Other pupils include Francesco Allegrini da Gubbio, Guido Ubaldo Abatini, Vincenzo Manenti, and Bernardino Parasole.