A number of the ground-floor rooms house a remarkable collection of panel paintings by Fra Angelico: particularly fine are the Last Judgement, the Linaioli Tabernacle, the Deposition, the Silver Wardrobe doors.
The San Marco Museum also houses a number of works by Fra Bartolomeo (1472-1517), including a famous portrait of Savonarola.

The Library, the first Renaissance library open to the public, formerly held the Italian, Latin and Greek codices that belonged to the Humanist, Niccolò Niccoli, which later passed to the Laurentian Library.
It now holds a precious collection of over a hundred illuminated choir books from the Middle Ages and Renaissance, originating from this monastery and other suppressed monasteries and convents.