It was built on the ruins of the Quetzalcoatl temple in a neoclassical style by indigenous hands under the direction of Friar Toribio de Alcaraz.

It includes chapels, an atrial wall, the temple, the atrium, the cloister, the Chapel of the Natives, and the Chapel of the Third Order.

The Royal Chapel or Chapel of the Natives was constructed before the convent, in 1540, with the purpose of indoctrinating the indigenous population. Its construction features Moorish influences and boasts an astonishing ceiling composed of 49 domes covering the seven naves of the temple. The baptismal font, dating back to the 16th century, is a notable feature.

The Chapel of the Third Order is more modest but has a beautiful Baroque facade. Inside, its altars are in a neoclassical style, and the dome is adorned with paintings of notable Franciscans.

Within the cloister, there are some colonial-era frescoes and a painting depicting a passage from Saint Francis of Assisi. Part of the original floor is still preserved.

In the convent's porter's lodge, there is a small gallery of Sacred Art showcasing some religious artworks.