A dynastic library, it houses the book collection of the Este family, the earliest traces of which date back to the 14th century.

Under the impetus of Marquis Niccolò III, it took on the appearance of an important humanist library, rich in works of literary, historical and artistic content, and its endowment grew considerably during the humanist and Renaissance periods with valuable manuscripts and fundamental printed editions, thanks to the refined and attentive collecting vocation of the Dukes of Este.
In 1598, the Library followed the dynasty in the transfer of the capital from Ferrara to Modena.
In the following centuries, the Biblioteca Estense continued to be enriched with works of local and international character, with funds deriving from the suppression of religious orders and from bequests and acquisitions also due to the enlightened activity of famous librarians such as Ludovico Antonio Muratori and Girolamo Tiraboschi.

Following the move to the Palazzo dei Musei, the Estense Library merged with the University Library. In 1995 the Estense University Library was established, since 2015 part of the Estense Galleries.