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.

The upper floor of this cloister was built between 1750 and 1774. This level originally housed classrooms, the antechapel, the guardian’s cell, and the bell-ringer’s cell. Over 105 years, these spaces underwent various changes in use, with only the bell-ringer’s cell remaining intact. Like the ground floor, the arcades were originally open; the walls that now enclose the arches were likely added when the building was converted into a museum in 1917, possibly to create more wall space for displaying paintings.

The Franciscan order strongly promoted reflection on Christ’s suffering and death. The paintings in this cloister served as tools for the friars and novices to meditate on the Passion, a term derived from the Latin flagrantia, meaning ardor or pain. The series consists of 29 scenes, from Christ’s triumphant entry into Jerusalem on Palm Sunday to His burial. The artist includes the trial of Christ and all 14 Stations of the Cross.

Each canvas features inscriptions, including rhymed verses commenting on the depicted scenes. Some paintings bear the abbreviation A dev. de (“Out of devotion from”) followed by the name of the donor, including clergymen from Durango, San Miguel el Grande (now San Miguel de Allende), and residents of Villa de Guadalupe. These inscriptions were likely added during the 19th century.

The word cloister comes from the Latin claustrum, meaning a space open to the sky and closed to the world. This cloister was dedicated to Saint Francis of Assisi, founder of the Franciscan Order, and was built between 1750 and 1775. At its center is a courtyard and a cistern completed in 1881.

It contains 26 oil paintings on canvas created specifically for this space, depicting key moments in the life of Saint Francis. These works were valuable pedagogical tools for the daily instruction of those living at the Colegio de Propaganda Fide in Guadalupe, Zacatecas. This series is of great significance: though similar collections existed in other New Spanish convents, this is the only one preserved in full and in its original location. Each painting includes explanatory verses and the name of the benefactor who funded its creation. The artist portrays Saint Francis not only as the founder of a religious family but also as a model for men and women of his time. The images depict biographical episodes and miracles attributed to him.

The iconography of the cloister carries an allegorical message encouraging the imitation of Christ. Each canvas reflects the Baroque spirit of the time, with open compositions that convey movement and draw the viewer into the scenes, turning them into witnesses to the saint’s life and deeds.

Together, these paintings form a rich tapestry of Franciscan existential scenes, expressing the founder’s ideals: emulating Christ and the apostles through a life of individual perfection and poverty, combined with a broad popular mission to save souls—both faithful and non-believers—while maintaining strict obedience to the Catholic Church.

In the viceregal period, convent churches reserved an upper level opposite the main altar for the choir. This was where the religious community gathered to chant psalms, hymns, and prayers at designated hours, following the rules of their order. Some of these choir lofts, such as the one in the Colegio de Guadalupe, were furnished with carved wooden choir stalls adorned with Marian symbols. Between each stall stand full-body sculptures of various saints. At the center, a wooden lectern (facistol) held large choir books containing the community’s sung prayers.

Though the artists responsible for Guadalupe’s magnificent ensemble remain unknown, the quality of the carving and polychromy can still be admired in its original location. Among the depicted saints are apostles holding the instruments of their martyrdom, interspersed with Marian symbols from the Litany of Loreto. At the center stands a life-size sculpture of Saint Francis of Assisi. Unlike the other painted and gilded sculptures, this one was designed to be dressed and includes a mechanism allowing it to be positioned seated or standing, depending on the needs of various ceremonies.

The walls of this space are adorned with large-format paintings that reflect Franciscan devotions, including Saint Joseph and a Franciscan allegory depicting the battle against heresy, located on the main wall.

The upper level of the building was constructed between 1750 and 1774. Its walls are decorated with monumental paintings by some of the most renowned 18th-century artists, including Miguel Cabrera, José de Ibarra, and Nicolás Rodríguez Juárez. Three of the largest canvases—by Cabrera and José Ríos Arnáez—were designed specifically for this space. This iconic area of the Museo de Guadalupe exemplifies the splendor of Mexican Baroque art.

The building is unique among the former Propaganda Fide Colleges in that much of its original artwork remains in situ. The grand staircase, choir, and upper and lower cloisters all bear witness to this remarkable preservation.

The "portería" served as the threshold to the Colegio de Guadalupe and was likely built after 1775, when the cloisters of the Passion of Christ and of Saint Francis were completed. It was customary at the time to add the portico as the complex expanded. This space was overseen by the porter father, who played a key role as the eyes and ears of the guardian.

The porter kept track of friars who left the college and laypeople who occasionally entered, and he also reported on missionaries who, for various reasons, needed to stay overnight.

In this room stands the frontal of a Neoclassical altar. Recent research suggests that during the Reform era (1856–1859), the college was partially divided, with one section remaining under Franciscan care. During that time, this room may have functioned as a small chapel reserved for the friars. In 1878, the Franciscans ceded the porter's lodge, the upper and lower cloisters, and the choir to the government of Zacatecas. The topographic survey for this division was carried out by surveyor Sixto Espinoza.

Here you can also find portraits of the founders of the Colegio de Guadalupe: Friars José Guerra, Antonio Margil, and Pedro de la Concepción y Urtiaga.

The word devotion is understood as “love and veneration, religious fervor, non-obligatory pious practices; a special inclination or fondness, and generally, a good custom.” This concept defined the society that, by the 18th century, was fully established in what is now Mexico, then known as New Spain. The prevailing mindset revolved around salvation and sacrifice, regardless of economic status or ethnicity.

During the Baroque period, devotion and the veneration of saints, biblical narratives, and religious icons as life models were further intensified. This fervor nourished imagination and sensibility through beliefs, traditions, and customs that still endure today.

The founding decree of the College of Guadalupe, dated 1704, mentions that the apostolic work was mainly directed toward the province of Coahuila and also to the lands of Texas. Typically, around 30 religious men lived at the College, and the friars who went out to evangelize had to spend at least two years preparing within this institution.

The first missions were led by Friar Antonio Margil de Jesús along the banks of the Sabinas River in Coahuila, but the hostility of the indigenous people prevented them from thriving. Nevertheless, the friars' determination was not deterred. By 1716, they had established some missions along the San Antonio and Guadalupe rivers in Texas and even managed to reach the borders of French Louisiana. By the late 18th century, they had also founded over 14 towns in the Mexican Gulf Coast region (present-day Tamaulipas), took charge of 15 missions left by the Jesuits in the Sierra Tarahumara, and reached Alta California. Thus, the work of the missionaries of Guadalupe is reflected in more than thirty mission foundations, covering much of the northern frontier during the colonial period.

In the Colleges of Propaganda Fide, three mandatory courses were taught: theology, the arts or philosophy, and grammar. Special emphasis was placed on theological studies, which were considered essential for the training of those who would evangelize the unconverted. One of the most studied authors was the Franciscan saint, Saint Bonaventure, also known as the "Seraphic Doctor," particularly for his book "The Mirror of Regular Discipline".

Due to its importance, the theology hall had to be located in the cloister, within the main core of the College. A "small pulpit" was also placed so that sick or elderly friars could attend religious services without needing to go down to the temple.

In the 18th-century intellectual world of New Spain, the Colleges of Propaganda Fide, dedicated to the training of missionaries, placed equal value on the study of theology and philosophy. Among the most significant figures in the field of philosophy was the Franciscan Juan Duns Scotus (1266-1308), known as the “Subtle Doctor” for his writings that emphasized the Immaculate Conception of the Virgin Mary. In the Library of the College of Guadalupe, there are works by him urging the Franciscans to attain Christian perfection. This serves as a testament to the importance of certain authors in the formation of missionaries.

This space originally served as the vestibule for the adjacent classroom and small pulpit. After 1859, due to the reduced number of friars residing at the College, philosophy classes began to be held in this very room. Later, at the end of the 19th century and during the first two decades of the 20th century, an improvised pharmacy was set up, which included some of the medicinal herbs that are now on display.

The exhibition room dedicated to the Camino Real de Tierra Adentro showcases eight modes of transportation from the 18th to the 20th centuries. Through these objects, visitors can observe how the discovery of silver mines in Zacatecas was a powerful motivator for the Spanish to venture into the northern regions of New Spain. The Camino Real de Tierra Adentro, which extended from Mexico City to Santa Fe, New Mexico in the United States, played a crucial role in this expansion. The College of Propaganda Fide was funded by influential miners such as Ignacio Rivera de Bernárdez and Francisco Xavier Aristorena y Lanz.

The Franciscans of the Apostolic College of Propaganda Fide of Guadalupe, Zacatecas, played a leading role in this effort. From there, numerous groups of friars set out to establish missions in northern Mexico and present-day southern United States along the Camino Real. During their long journeys, they conducted mass baptisms and preached the gospel to the local inhabitants. This work was not easy, and many times they faced failure and martyrdom; however, their determination led them to the farthest regions of the Viceroyalty, including Texas and New Mexico.

In 1521, the slow process of colonization and Christianization began on the Philippine archipelago, named in honor of Spanish King Philip II when Spain conquered and colonized the Asian region. The Philippines maintained a close trade exchange with New Spain through the Manila Galleon, which sailed from the port of Acapulco to Manila.

Following this route, in 1596, the Spanish ship "San Felipe", traveling from Manila, Philippines to Acapulco, was shipwrecked off the coast of Japan. When the ship's captain, Francisco de Landa, was captured, he was brought before the emperor, Tagcosama, and declared that the Franciscan and Jesuit missionaries were advancing to facilitate the Spanish army's invasion. The ruler's reaction was so strong that he ordered his shogun, Toyotomi Hideyoshi (the general in charge of fighting the barbarians), to arrest three Jesuits, six Franciscans, and 17 Japanese Christians. These individuals were transferred through various towns during the winter, covering 800 kilometers, and were tortured by having one ear cut off as a symbol of humiliation, intended to show the population the punishment for Christian converts. Ultimately, they were bound to a cross and pierced with two crossed spears in Nagasaki in 1597. In 1862, the 26 prisoners were canonized as the "Martyrs of Japan."