The church dates back to the 9th century and belonged to the Frisians and their schola. In the early Middle Ages, in fact, several ethnically-based scholae sprang up in this area, i.e. associations of a charitable and welfare character for pilgrims coming to Rome to visit the tomb of St Peter. The schola of the Frisians therefore founded the church, dedicating it to St Michael the Archangel. The primitive church was destroyed in the fight to free Gregory VII between Robert Guiscard and Emperor Henry IV, who resided in the schola of the Frisians.

The new church was built in the 12th century and also took the name of St Magnus, welcoming his relics; it was on this occasion that the Romanesque bell tower was added, today only visible from St Peter's Square. It then underwent restorations over the following centuries, especially in the 18th century by Carlo Murena, while retaining its medieval structure.

Access to the church is via a staircase, in the past considered holy. Internally, it has three naves, divided by ancient columns enclosed within 18th-century pillars. In the nave, what remains of the ancient Cosmatesque floor is preserved.

Two mediaeval plaques are preserved in the church: the first informs us that the present altar was consecrated by Innocent II on 30 January 1141; the second recounts the miraculous event of the discovery of the relics of St Magnus in Fondi and their translation to Rome.