Formerly known as the Church of Nossa Senhora da Conceição do Colégio dos Jesuítas or as the Church of the Seminary.
The current Santarém Cathedral is a 17th century temple erected on the site where the Royal Palace of Alcáçova Nova once stood, a royal residence that It had been abandoned, during the time of D. João II (15th century).
In 1647, King João IV donated the ruins to the Society of Jesus so that it could create a school there with a church dedicated to Our Lady of Conception.
In 1780, after the expulsion of the Jesuits from Portugal, Queen Maria I donated the buildings to the Patriarchate of Lisbon for the installation of her Seminary. With the creation of the Diocese of Santarém on July 16, 1975, the church was elevated to a Cathedral.