The church, started in 1774, is one of the main landmarks of Brazilian colonial art, becoming famous for the beauty of its architecture, the richness of its carving, and the work of Aleijadinho, later modified by Francisco Cerqueira.

The history of the Saint Francis of Assisi Church dates back to March 8, 1749, when the Secular Franciscan Order was founded,[2] and canonically erected by the then Bishop of Mariana, Friar Manoel da Cruz.

Aleijadinho was hired to design the structure and decoration, and in 1774 Francisco de Lima Cerqueira was commissioned to begin the masonry work, but he introduced modifications to the towers, the pilasters of the crossing, the glasses of the nave, and the arrangement of the sacristy.

[3] By 1804, the nave and the other works in the body of the church had been finished and in 1809, Aniceto de Souza Lopes completed the towers and the choir, besides executing, according to IPHAN, the reliefs of the pediment and the frontispiece of the gate.

[3][5] His authorship is assured by the survival of an incomplete autograph drawing of the front elevation of the building, today preserved in the Inconfidência Museum in Ouro Preto.

[2] There appear the winged coats of arms of the Franciscan Order and the Kingdom of Portugal, on which a medallion bears the image of the praying Virgin among garlands and under a royal crown, from which hangs a banner with the Latin words Tota pulcra es Maria et macula originalis non est in te ("You are all beautiful, Mary, and you are free from original sin").

"[8] Aleijadinho was one of the responsible for the elaboration of a new style in Minas Gerais, which shows the first signs of the formation of a genuinely Brazilian aesthetic, and which has no direct precedents in Portugal.

[4] Mário de Andrade, one of the most noted modernists engaged in the study of the colonial past, when this topic appeared at the beginning of the 20th century as a fulcrum for the nationalist aspirations of intellectuals and the search for the "true" cultural identity of the country, stated:[9] "Aleijadinho, arising from the lesson of Pedro Gomes Chaves, comes to genialize his manner, creating at the same time a typical church which is the only original solution that Brazilian architecture has ever invented.

"The modifications introduced by Cerqueira, although considerable and object of great controversy,[6][10] contributed to an increase in its originality, particularly in the solution he found for the towers, as pointed out by John Bury, who is one of the basic references for the study of colonial art in Brazil.

[4] Early scholars of the Brazilian Baroque, such as Lúcio Costa and Germain Bazin, tended to consider Cerqueira a traitor of Aleijadinho's legacy, and some still think so today, but his contribution has been reviewed, notably by Myriam Ribeiro de Oliveira, among others, as an important collaborator and a creative artist in his own right.

"[6] Still, in Oliveras' opinion, "what is extraordinary, in our view, is that the extent of these modifications has resulted in a work of such quality, produced by the sensitivity and technical expertise of Lima Cerqueira, and should consequently be evaluated in its values and not compared to an initial project that was not obeyed, as has been done until today",[6] and for Bury, the Church of St. Francis shows "an exceptionally high artistic sensibility in its design and decoration".

According to IPHAN, the sculptural group that crowns the frontispiece, with a representation of the Holy Trinity that has similarities with the solution that Aleijadinho gave to the altar of the church of the same name in Ouro Preto, is a highlight.

[13] As in other places in Minas Gerais, the celebrations of Holy Week have special relevance in São João del-Rei,[15] and the Francis of Assisi Church takes an active part in the solemnities.

Such festivities usually have large popular participation and feature music by colonial and contemporary authors, including pieces composed especially for local Franciscan worship.