The Colegio de Propaganda Fide housed several libraries: the "Librería Guadalupana" (the main or common library), the novices’ library, and individual collections belonging to each friar. Together, they amassed over 30,000 volumes. More than 9,000 of these books are still preserved and on display, most of which were acquired by the Franciscans after the period of cloistering. A significant portion of the collection is written in Latin, Spanish, and other European languages.

According to the statutes of the Propaganda Fide branch of the Franciscan order, novices underwent at least six years of preparation. During this time, they studied a wide range of disciplines, including philosophy, theology, physics, cosmology, and native languages. Future missionaries first read liturgical books and the Bible, followed by theological works and, eventually, the lives of saints. The library, often referred to as the "librería antigua", was considered a privileged space for safeguarding knowledge. The foundation of this library is credited to Friar Antonio Margil de Jesús, who requested the first shipment of books.

Among the most notable titles are the Bible, the Council of Trent, the Mexican Provincial Council, "Mystical City of God", and "The City of God"". The topics covered are diverse, including hagiography, asceticism, catechetics, canon law and other religious subjects, as well as algebra, geography, physics, philosophy, chemistry, natural history compendiums, atlases, moral theology, zoology, astronomy, Latin grammar, and the history of Mexico, among others.