The church and monastery of Santa Maria in Organo were founded by Benedictine monks in the 8th century as a dependency of the Patriarch of Aquileia. The name may derive from the organum, a local device that drew water from the Adige. Between the 11th and 12th centuries, the church was rebuilt, with three naves and semicircular apses, and an oratory crypt. In the 15th century, the complex passed to the Olivetan Benedictine monks, who began a reconstruction of the church and monastic residences, summoning the best artists in the city (Domenico and Francesco Morone, Giovanni Francesco Caroto).
Between 1494 and 1499, the Olivetan friar Giovanni da Verona built the wooden choir, which has 41 stalls inlaid with figures of saints and scenes carved in perspective. A large lectern bearing the figure of a rabbit was placed in the centre, in 1501. Between 1519 and 1523, when Cipriano Cipriani was abbot, Giovanni created the sacristy. It has a ten‑metre‑long panel board depicting architectural scenes, liturgical objects and work tools, which Giorgio Vasari considered the most beautiful in Italy. Friar Giovanni's inlaid mirrors are a masterpiece of the Renaissance period.
The façade of the church, reminiscent of Leon Battista Alberti's Malatesta Temple in Rimini, features three deep arches and pilasters connected to Corinthian columns. It was designed from 1546 onwards by Michele Sanmicheli, the great Veronese architect of the time. The upper part of the façade, in which the Romanesque wall of bricks alternating with stone can be seen, was never completed.