The restoration process started with a comprehensive study using various techniques such as ultraviolet radiation testing. These chemical tests led to the important finding that the paintings were made in mixed media.

The project had several stages including strengthening the interior walls (1993), restoring the paintings in the central nave (1997) and in the side naves and the railing (1999).

The second phase saw the removal of the Baroque cornucopia which was moved to the sacristy to decorate the copy of the Last Supper in the tabernacle found there.