For Marsili, an extensive library was supposed the center of activity of the Istituto delle Scienze.
Consistently with that commitment, he made available part of his wealth and all his international contacts to promote the ongoing influx of new books from all over Europe.

Just a few years before his death, when his volume Danubius Pannonico-Mysicus was re-issued, Marsili made a special contract with the Dutch publisher so that in lieu of paying the author, the publisher would provide the Palazzo Poggi library with the works that Marsili considered “useful for the institute".

Similar concerns had long troubled Pope Benedict XIV. With his encouragement and special funding, construction of the magnificent great hall, the Aula Magna, was completed in 1744 on the piano nobile of the building in 1744. The hall would finally make it possible to house and catalogue the volumes already owned by the institute as well as newly acquired ones.

The earliest library of the Istituto delle Scienze, which has been in operation since 1724 is today part of the museum open to the public.