The current structure of the church was defined during the last important works done in the 2nd half of 19th century, with the final arrangement of the east facade and the enlargement of the interiors. A new aisle, with three chapels, was added on north, giving to the construction an asymmetrical aspect. As a matter of fact, it was not possible to reach anymore a perfect symmetry because of the landslides which affected the hill: nowadays the church ends right on the edge of the cliff. Some medieval documents attest that before there were some terraced vineyards between the church and the precipice. The natural erosion and the exploitation of the tufa mine below caused the slides.

The Benedictine Abbey of San Michele has not been the only monastery in Terra Murata: in 1585 the Cardinal Innico of Avalos allowed Dominican monks to move their friary from Santa Margherita near Chiaiolella (on the promontory in front of Vivara) to the south edge of Terra Murata (from then on called "Punta dei Monaci", Cape of the Monks). The new monastery was named Santa Margherita Nuova (New). The static failures suffered by the building because of the friability of the underlying tufa rocks required the monastery to be abandoned, and it was not reopened anymore.