The tapestries housed in the Cathedral Museum are of particular interest and include the series of six works illustrating the Stories of Moses, plus another tapestry with the Dance of the Putti, all given to Carlo Borromeo by Guglielmo I Gonzaga, Duke of Mantua. In 1568 Borromeo donated them to the Fabbrica in exchange for work in the presbytery.

Three of these tapestries were destroyed in the fire at the Milan Expo of 1906: Moses before the Pharaoh, the Jewish Easter and the Gathering of the Manna. One room of the museum is dedicated to the surviving tapestries and here visitors can admire the Crossing of the Red Sea, Moses and the bronze serpent, Moses with the tables of the Law and the Dance of the Putti.