At the beginning of the 1990's it was decided to undertake a reorganization of the Accademia's entire historical patrimony, including the musical instrument collection. Extensive documentation, research and investigation were begun. All the instruments were evaluated for their state of conservation; where necessary, protective repairs were made.

To make the collection immediately accessible to a broader public, some of the most important instruments were selected for exhibition in 1993. A special catalogue was published on that occasion, entitled "Il liuto e la lira. Verso un recupero del Museo Strumentale dell'Accademia Nazionale di Santa Cecilia"(The Lute and the Lyre. Regarding the restoration of the Musical Instrument Museum of the Accademia Nazionale di Santa Cecilia). Meanwhile, a new drive was launched to attract donations and to purchase pieces for the Museum. Thus, it acquired several ethno-organologic sets (including instruments collected by composer Enrico Terni) and a number of individual instruments from the western classical tradition, along with tools and other items from the workshop of Roman luthier Rodolfo Fredi. The latest acquisition dates from early 2007, when luthier Dante Regazzoni's heirs donated their father's workshop to the Museum.

These diverse activities continued throughout the ensuing decade, during which a more stable arrangement was being planned which would include showcases designed to guarantee maximum conservation of the instruments. At the end of 1999, on the eve of the Jubilee Year, a new exhibition was opened in the rooms at Via della Conciliazione. Meanwhile the Accademia di Santa Cecilia was close to obtaining a new site which would finally bring all the foundation's activities together in new quarters at Auditorium Parco della Musica. Thus the Accademia and its entire heritage began the lengthy move to its current home, along with a complete reorganization.

An initial, extremely "staged" exhibition of the musical instruments collection was set up in Spazio Risonanze; the instruments were displayed next to drawings by Paul Klee and a work by Alexander Calder, Humtulips. But a specially designed space had been hypothesized from the very beginning - a space more suited to exhibiting the permanent collection and more befitting the scientific and educational tasks natural to a museum. Some years later, architect Renzo Piano translated this idea into a new plan.

In a 2004 interview, Piano said, "I got the idea that entering the exhibition of the instruments ought to be like entering a vault, the safe containing the Auditorium's treasures."

Today, the "jewels" the Accademia di Santa Cecilia has collected over the centuries are at home in their new "treasure chest", where they can be preserved with proper care and admired by the many enthusiastic music-lovers who attend Accademia activities and concerts at the Auditorium.