In 1542, the monk Juan de San Miguel founded the San Miguel mission by the river of the same name (now Rio Laja) at the site currently known as San Miguel Viejo. In 1551, after an attack by indigenous people, the mission was moved further east from its original location under the leadership of the monk Bernardo de Cossina, who established it at a place known as Iscuinapan. The monk Gonzalo de las Casas, who wrote his "News of the Chichimecas" for Viceroy Enríquez (1568–1580), claimed that “... the fathers of the Order of San Francisco founded a monastery in the villa of Señor San Miguel, where many people from the Guamar Chichimecas gathered, and with them were settled the Otomi and Tarascan Indians...”.

This monastery, undoubtedly modest given the poverty of the village and only ten years of history of baptizing indigenous people, was attached to the San Miguel mission. Two years later, in 1564, the mission was transformed into a parish by order of the Basque bishop Quiroga, and the former monastery changed its name and became a parish, thus concluding the missionary work of the first Franciscans. From that moment, the ancient monastery ceased to appear as such in the province’s chronicles. Returning to the villa of San Miguel, in 1606 they resumed their work, interrupted almost half a century earlier. They dedicated their efforts to the Christianization of the simple rural inhabitants. In the villa, they began construction of a chapel and an adjoining monastery. Soon a modest monastic complex arose, which has been preserved to this day with minor changes. Its church, originally built as the Church of Saint Anthony, is now known as the Third Order Temple. The monastery was renamed the Monastery of Saint Francis, and thus the church, which currently dominates the complex, bears this name.

The monastery is located north of the Third Order Temple. Its heavy construction, devoid of Baroque ornamentation, places it among buildings constructed during the transitional period from Renaissance to Baroque. Construction began in 1606 and was interrupted in 1638, then resumed in 1680, but now fully in the Baroque style. By the end of the century, the monastery was improved and expanded, and the first Church of San Francisco was built, positioned relative to the monastery so that it adjoined the inner courtyard, which was enclosed by a crenellated wall with two entrance arches: one to the south, connecting to San Antonio Street (today San Francisco), and another to the east, connecting to Ascapotzalco Street (today Juárez).

Work continued until the early eighteenth century, and in 1713 the main altar was re-consecrated, according to a document from the Oratory archive, where parishioners were invited to attend the ceremony. It was in this year that some changes were made to the main façade, in particular, a spire was installed, which serves as the church’s bell tower. The original Church of Saint Francis was demolished by 1779, as from March 2 of that year, the book recording donations “for the construction of the church being carried out in the Monastery of Saint Francis” notes contributions for the building’s construction and expenses. This construction lasted twenty years and was completed on April 13, 1799, when it was consecrated.

Those who like to classify architecture will face difficulties with the Church of Saint Francis. One expert says its façade is Baroque, another says pure Churrigueresque, another Rococo, and yet another believes it is a combination of all these styles. In any case, the façade facing the small San Francisco square is elaborately detailed and richly decorated. The upkeep of the Church of Saint Francis was partially funded by donations from local families and partially by funds obtained from bullfighting events.

The Franciscans especially venerate the saints carved in stone on the pediment, with Saint Francis at the very top. The most interesting works are the crucified Christ, the Immaculate Conception, Saint John, and the Virgin Mary. The eastern façade continues the combination of religious sculpture with pure design. Its marvel lies in the stonework, an art that reached its peak here near the end of the eighteenth century. Sculptors of that era achieved the lightness of lace and the richness of brocade. The single tower elegantly rises above the gray battlements, built in the Neoclassical style, with Moorish influence felt in its design. It stands out against the sky with its octagonal dome, topped by a sphere, above which rises the patriarchal cross with two brackets and an eighteen-pointed weather vane, resembling a huge finger pointing to infinity. This work is attributed to the famous Celayan architect Eduardo Tresguerras. Inside, Ionic and Corinthian order columns are used. Other sources attribute the mentioned façade to Don Lorenzo Rodríguez, author of El Sagrario and La Santísima in Mexico City. Next to the church is the Monastery of Saint Francis, built in the early sixteenth century, where some wall paintings still remain. Originally, it was known as the Monastery of Saint Anthony.

Its exterior suggests the Spartan simplicity of the Franciscans who built it. Although there are several excellent paintings and frescoes, the main interest lies in comparing it with the church next to it. They are separated by a century and a half, and one can see the transition from an innovative society to a wealthy community at the height of the world and prosperity, and simultaneously despotism — which would soon be destroyed by revolution.

The upkeep of the Church of Saint Francis was partially funded by donations from local families and partially by funds obtained from bullfighting events. The building was continuously constructed over twenty years; the first stone was laid on June 29, 1779, and construction was completed on April 13, 1799. It has a single tower in the Neoclassical style, although it also shows some Moorish influence. This work is attributed to the famous Celayan architect Eduardo Tresguerras.

Inside, you can admire various styles and different pictorial works.

Sources:

https://www.de-paseo.com/san-miguel-de-allende/item/templo-de-san-francisco/#

https://www.atencionsma.com/columnistas/luis-felipe-rodriguez/la-construccion-del-templo-de-san-francisco-en-san-miguel-de-allende/