One of the great treasures of San Carlino is its historic library. It was designed and built as an integral part of the convent by Francesco Borromini himself between 1635 and 1641. The author conceived it as a spacious, well-lit, quiet and comfortable area, and designed it as a quadrangular space measuring 18.30 x 5 meters.

In the 1670s, Bernardo, Francesco Borromini's nephew, who continued the work at San Carlino after his uncle's death, halved the height of the library windows and converted the central window leading to the dome and the bell tower into a door.

In 1897 the shelves had to be extended to cover the side walls to make room for a large collection of books donated by the Spanish canon Josu00e9 de Benavides.

In the mid-19th century a plaster bas-relief was made by the sculptor Aniceto Marinas, commissioned by the archaeologist Giovanni Battista Rossi. It depicts the visit of Pope Pius IX to the catacombs of St. Callixtus, which he discovered. It is probably a donation by Josu00e9 de Benavides himself.

From 1986 onwards, a series of improvements were made to the library by the Ufficio Italiano dei Cambi (Italian Currency Exchange Office), part of the Banca d'Italia (Italian National Bank), in collaboration with the Italian Ministry for Cultural and Environmental Heritage.

The work included improving the waterproofing of the roof, the restoration of the original ceiling and floor, the disinfection of furniture and books, implementing fire and safety measures, and the renovation of the electrical installation.

At the end of the 1990s, Juan Maru00eda Montijano, professor of Art History at the University of Malaga and a great connoisseur of Italian Renaissance and Baroque architecture, upon discovering the wonders of San Carlino and, in particular, the enormous potential of its library, devoted himself with true passion and generosity to its restoration. Initially, he dedicated himself alone and altruistically to the conservation of the library, initiating the process of cataloguing its bibliographic content.

In 2012, Montijano sponsored the signing of an agreement between the Trinitarian community of San Carlino and the University of Malaga, in collaboration with other cultural entities, for the cataloguing of the bibliographic collection by scholarship students from the Faculties of Art History, History, Fine Arts and Architecture of that university.

These students, hosted by the religious community, carried out this work during the summer, with real care and affection, and under the professional and attentive direction of the aforementioned teacher. The cataloging was completed in 2015.

During this time they inventoried more than 13,000 volumes written in 16 different languages, predominantly Latin, Italian and Spanish. The works in question are dated as follows:
- eight incunabula,
- 786 books of the 16th century,
- 2.962 of the X17thVII century,
- 3,722 of the 18th century,
- 4,921 of the 19th century,
- 250 outstanding books of the 20th century;
- several manuscripts.

Most of the books are of a philosophical and theological nature, or on different humanistic disciplines (art, geography, history...). In addition to the eight incunabula, the bibliographical treasures include a polyglot Bible from the beginning of the 16th century and a copy of the first illustrated edition of Don Quixote, as well as several books whose only preserved copy is the one in this library.

A computer program was used in the cataloguing process, which allows researchers from all over the world to consult them. In addition, several works of special value were scanned, including the Libro de fu00e1brica de San Carlino.