It was built by Daniel de São Francisco, a Franciscan friar born in Penafiel, Portugal.

Daniel de São Francisco taught theology in Salvador for many years, and was then chosen to negotiate the separation of the Brazilian Franciscan convents from those in Portugal.

Its design likely influenced the Convent and Church of Saint Antony in Iguape, Cachoeira, which was completed by 1680.

Alberto Sousa asserts that the church is the first in Brazil to exhibit Baroque features, and predates the introduction of the style in Portugal.

The partially-constructed building fell into decay in the 19th century; its ruins are located to the north of the site.