In 1996, a renovation strategy was developed with a historical approach: the building's exterior was of primary historic importance, while the interior would be a blend of historic restoration, historically sensitive renovation, and transitional design. A detailed Restoration/Renovation Program was developed: while the public spaces would be a historic restoration/preservation effort, the office area challenge would be to develop a historically sensitive environment accommodating modern office requirements allowing for future flexibility.

Masonry cleaning began and efforts were made to duplicate crucial aspects of the exterior. The original slate roof was replaced. The decorative sheet metal on the roof (the window hoods, trim, and cornices) were removed, rebuilt in a local metal shop, and replaced. Interior mural restoration moved forward, documenting any mural work uncovered.

The interior phase of project included structural modifications, finishes, exit stairs, historic wood stairs, elevators, window replacement, mechanical systems, fire protection systems, toilet rooms, electrical systems, and site work.

The nine-year renovation process ended with the reopening of the Main Administration Building in the summer of 1999. Ceremonies were held in October of that year to welcome the restored building back to its place as the heart and soul of campus. "There's an elegance to the building that was hidden by the dust of years in the past," the Vice President of University Relations says. "I think it stands for the progress of Notre Dame. Just seeing it now, you realize this is the Main Building. This is the heart of the University, and this is where the University began."