As with old monastic constructions in Europe, the atrium was not absent. Architecturally, it resembled its European counterparts, but the difference lay in its functions: it was a multifunctional space used for doctrinal instruction, with a stone cross at its center, a cemetery, an open chapel, a cistern, and four "capillas posas" (wayside chapels).

This area stands out for its gargoyles—whimsical figures that create a visual harmony in combination with the soft arches and slender double columns that break the otherwise sober design of the complex.

The gargoyles served to channel rainwater from the roof or upper floors of the convent down to the courtyard drains and into the cisterns. Artistically carved as infernal creatures, they served as a reminder of the constant presence of evil in the world. This is why the word "gargoyle" is often associated with demons or monsters today.

Comprising corridors, arches, courtyard, cistern, "sala de profundis" (mourning room), refectory, storerooms, kitchen, stables, and gardens.

The courtyard collected rainwater into a large cistern from which water was drawn via a well. The corridors were used for walking and meditation; the refectory was the communal dining area; nearby were the kitchen, storage rooms for food and utensils, stables, workshops, and gardens.

The mural paintings throughout the corridors and spaces of the convent were important visual documents depicting biblical scenes, the lives of saints, and notable Church figures. The murals in the lower cloister focused on the Passion of Christ (lunettes at the arc corners), Saint Augustine (niches on the south wall), the apostles (medallions on the frieze near the top of the walls), and the monograms of Jesus and Mary.

A 16th-century confessional interrupts the molding on the north wall.

The friars cultivated a wide variety of vegetables and fruits. From Europe, they introduced lettuce, cabbage, radish, lentil, turnip, eggplant, garlic, onion, broad beans, and chickpeas. Native crops included corn, beans, chili, "quelite", squash, maguey, and "nopal". They also planted American fruit trees such as sapote, "mamey", "capulín", pineapple, avocado, and guava, as well as European species like peach, fig, pear, apple, pomegranate, quince, orange, watermelon, lemon, and banana.

The façade was designed to indicate that the church was dedicated to Saint Mary Magdalene. Although the Augustinian friars preached poverty, they believed that the monumental scale of the buildings, with their intricate carvings, made a lasting impression on the faithful.

The porter’s lodge, also known as the pilgrims’ portal, was the space the friars used to celebrate Mass. Upon approaching the entrance portal of the convent, one can observe that the walls are decorated with paintings. These are called frescoes, as the technique used involved applying colored pigments onto freshly plastered walls so that the paint would be absorbed and last for a long time.

One of the scenes depicted on the northern wall is the Last Judgment. The inclusion of this theme reflects the missionaries’ emphasis on the fear of God, true conversion, and sincere repentance, all in light of the prophesied end of the world according to the Gospel of John.

This was a large dining room where all the friars gathered for their meals. Aligned with this area were the kitchen, storerooms for all kinds of foodstuffs, grains, and utensils, the stables, workshops, and the garden.