The church was built in the Baroque architectural style with several Tuscan elements, and is considered one of the best examples of Baroque architecture in Cuba. The building is mainly constructed from blocks of coral cut from sources in the Gulf of Mexico's ocean floor. Preserved marine fossils are present in the facade. As more and more of the indigenous people were converted to Catholicism, the need for churches grew quickly. One of the largest missionary groups on the island were priests of the relatively new Society of Jesus (Jesuits). Many requests for construction had been denied by Havana's fight Attorney General. After extensive petitioning and the purchase of a piece of land in the Plaza by Diego Evelino Hurtado de Compostela, Bishop of Santiago de Cuba, a permit was granted to these missionaries. The cathedral is set in the former Plaza de La Ciénaga. In 1727 plans to build a church, convent and collegium were approved and the project began to take form, even though the location was less than ideal.

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