Located on a hill overlooking the central Via XX Settembre, it is one of the most outstanding examples of Romanesque architecture in the city.

The most ancient document mentioning Santo Stefano dates from 965, although some scholars attribute its foundation in 972 to the then bishop of Genoa, Theodulf, who rebuilt it after a Saracen inroad.

The abbey was held by the Benedictine order of Columbanian monks of Bobbio from 972 to 1431, when Pope Boniface IX turned it into a commenda under Cardinal Ludovico Fieschi.

The dome is now in brickwork; it was rebuilt in the 14th century by abbot Niccolò Fieschi, and is octagonal in shape.

The lower section of the bell tower is of uncertain dating, but is commonly deemed to be antecedent to the current church, and that it was probably used as a defensive structure.