The church was built initially in the 7th century. It is dedicated to Moses since like the Byzantines, the Venetians often considered Old Testament prophets as canonized saints. It also honours Moisè Venier, the aristocrat who funded the reconstruction during the 9th century.

San Moisè is the parish church of one of the parishes in the Vicariate of San Marco-Castello. The other churches within the parish are Santa Maria Zobenigo, San Fantin, Santa Croce degli Armeni and the Basilica of San Marco itself.