The Basilica was designed by the architect André Soares and built in the 16th century, although it was not finished until the 20th century.

Its construction began in 1703 and was blessed on 27 October 1717, although the towers were still to be built and the statues placed in the respective niches on the façade.

These works were carried out in the 20th century, and the west tower was completed in 1964 by the benefactor António Augusto Nogueira da Silva, based on a project by the architect Alberto da Silva Bessa (Vila Nova de Gaia, 16 October 1911 – Vila Nova de Gaia, 1984), who was inspired by the towers of the Monastery of São Miguel de Refojos de Basto.

The statues on the façade – St. Filipe Néri and St. Martinho de Dume – were erected on 16 February 1964 and are the work of the sculptor Manuel da Silva Nogueira (born in Santa Cruz do Bispo on 10 October 1926).

On 15 March 1975, the Holy See granted the Church of the Congregados the title of Minor Basilica.