In the 1990s bishop Sergio Goretti, in addition to encouraging the regular daily opening of the old exhibition spaces, began to consider a reorganization that would be more appropriate for the museum's objects.

In the corridor are archeological displays of items found in the immediate area, including capitals sculpted in limestone, rediscovered in the crypt but originally from the cathedral, and datable to between the 8th and the 12th centuries.

[2] Originally these frescoes decorated an area above today's chapel of the Madonna del Pianto which corresponds to the old left apse of the cathedral that was separated from the rest of the church with the modifications of Galeazzo Alessi in the 16th century.

Inside the crypt is a Roman sarcophagus from the beginning of the third century depicting the myth of Selene and Endimone in which the body of San Rufino was originally placed.

The frescoes in this room recount the story of Christ's passion, and were removed from the oratory of the Confraternity of San Rufinuccio and were painted by Puccio Capanna and Pace di Bartolo.

Among the works conserved here is the silver bust reliquary of San Rufino made by Paolo Spagna, and the large, recently restored painting by Sermei of St Francis blessing the city of Assisi at his death.