Between 1662 and 1680 the church was built for Santo António’s congregation, until then located at the Chapel of Santo António do Penedo. The church and surrounding area were offered to the Congregation of São Filipe Nery dos Clérigos Reformados do Oratório, who altered the project between 1694 and 1703 and created an additional building to serve as convent. In 1829, through the windows of this convent, facing Praça Dom Pedro (today, Praça da Liberdade) the monks saw the hanging and decapitation of the Martyrs of Liberty, which they celebrated with Port wine and cake (pão-de-ló), cheering to Dom Miguel and the holy religion.

During the Siege of Porto (1832-33), this church became a military hospital and army storage facility. The extinction of religious orders was ordered by Dom Pedro IV in 1834. The convent and the tower were then sold to a private entrepreneur in a public auction. In 1836, the church returned to the Congregados Brotherhood, and was then recovered. The tower was demolished in 1842.