In 1876, the Jesuits proposed to Manila Archbishop Pedro Payo, O.P., the construction of a church honoring their founder, St. Ignatius of Loyola, echoing the style of the first 17th century church destroyed by an earthquake. The acclaimed architect Felix Roxas, Sr., hailed the new church, San Ignacio Church, as sueño durado or a "golden dream." Its neoclassical design, with twin towers and a charming courtyard adorned with wrought iron grills, was a remarkable achievement considering the limited space.

The church’s interior was a testament to Filipino artisans' skill. The bells and metal embellishments came from Hilario Sunico's foundry, while sculptors such as Francisco Rodoreda and Isabelo Tampingco created stunning marble and wooden artworks. San Ignacio Church was consecrated in 1889 amid a week-long celebration that highlighted its innovative use of electric lights on the façade. It became a spiritual hub for Ateneo students until a 1932 fire caused minor damage alongside the adjacent Ateneo building. Sadly, World War II's devastation in 1945 left the church in ruins after Japanese forces set fire to it during the Battle of Manila.

After the war, the Jesuits salvaged what they could, but the property eventually fell into private hands and decayed over time. In 1990, the Intramuros Administration (IA) acquired the site with plans to convert it into an ecclesiastical museum. Reconstruction efforts began in 2015, culminating in the reopening of the rebuilt San Ignacio as the Museo de Intramuros in 2019, showcasing the IA's collection of ecclesiastical artifacts and history.