The Querini Foundation's collection of drawings is composed principally of 34 antique works attributed to the  schools of Giovanni Bellini and Titian, as well as to Ludovico Carracci, Jacopo Tintoretto and Marco Ricci. These drawings were sold by Giulia Sudarovich to Giovanni Querini’s nephew in 1842.

Of this collection, The Coronation of Carlo Magno by Gian Francesco Penni is the most renowned. It was previously attributed to Raffaello, who has signed it. This drawing is most likely a sketch for the fresco of The Coronation of the Emperor, commissioned by Leo X for the private rooms of the Pope where Raffaello painted the Cycle of the Liber Pontificalis. Realized in brown ink, watercolour and white lead, it represents the coronation of Charlemagne by Leo III on Christmas night in the year 800. Penni has modernized the scene by depicting Renaissance architectural elements and clothing. Leo III resembles Leo X and Charlemagne is represented as Francis I.

The drawing collection has been recently enhanced with private donations of twentieth-century drawings by the "capesarini," and with an interesting nucleus of sketches for the restoration of the Querini Palace's ground floor by Carlo Scarpa dating to the early 1960s.