The church is one of the main elements of the Historic Center of Salvador and lies within the UNESCO World Heritage Site of the city.

A competition was held for its design, and on December 18, 1701, the Fathers of the Third Order chose Gabriel Ribeiro (late 16th century – 1719), a native of Porto, Portugal.

[1][2][4] Church of the Third Order of Saint Francis sits behind a small churchyard on Igreja da Ordem Terceira slightly removed from the Terreiro do Jesus.

The entrance hall has a collection of paintings depicting the life of Saint Francis by Bento José Rufino Capinam (1791–1874).

The Sala da Mesa, a large meeting room for the Brotherhood, is richly decorated with paintings and azulejos.

Polychromatic lioz limestone was imported at great expense from Portugal and is utilized in the decorative flooring of the nave, chancel, and sacristy.

Azulejos in the church complex also depict the marriage of Prince José, later Joseph I of Portugal, and Mariana Victoria of Spain in 1729.

A statue of Saint Francis of Assisi is in a niche at the upper center of the complex façade; it is likely of limestone imported from Portugal used in numerous churches in the same period.

The outer figures are Caryatids, and those closest to the niche, with a naked chest and wings next to the head, are representation of Hermes.

Its corridors are richly lined in azulejos, similarly to the cloister of the São Francisco Church; its columns are of local Bahian sandstone.

The processional saints, revered by the Franciscan order, and niches are the work of the master woodcarver Joaquim Francisco de Mattos.

The center of the lavabo has an inlay coat of arms of the Franciscan Order with stylized birds to the left and right.