The church is dedicated to Saint Michael (Roman Catholic), the holder of the scales on Judgement Day, a fit guardian of the sleep of the faithful dead.

However, the first documentation we have is that a church dedicated to St Michael was granted in 1212 to the monastic order under the assent of the Bishops Marco Niccola and Buono Balbi.

Placido Zurla, also a monk at San Michele, wrote an account of the map, titled Il Mappamondo di Fra Mauro.

San Michele is considered one of the first examples of Renaissance architecture in Venice, with a facade that appears influenced by the work of Alberti.

[8] The strongly delineated masonry courses[9] of the ashlar facade are carried right across the Ionic pilasters, a strikingly unusual feature for which that R. Lieberman could only find an earlier parallel in Bernardo Rossellino's Palazzo Piccolomini in Pienza, also of the 1460s, and also produced in an Albertian milieu.

When it was finished, a monk of the community wrote, "The facade, now complete and perfect, shiner of such a beauty so that it turns in itself the light of the eyes of all those who walk or sail by".

A description from 1868 recalls the decoration of the church included a Bust of Cardinal Giovanni Dolfin (1622), sculpted by Bernini, and located above the interior portal.