The land came from Juan Ponce de Leon. In 1522, a decade before the church was built, Ponce de Leon donated the site to the Dominican Order at what was then the northernmost edge of the newly established settlement of Puerto Rico de San Juan Bautista. The Dominicans built their convent and church in the Isabelline style -- a transitional form that blended late Gothic structure with early Renaissance ornament, characteristic of the reign of Queen Isabella I of Castile. The result was a building that carried European architectural ambition across the Atlantic, its ribbed vaults and pointed arches rising on a Caribbean hilltop. Doors made from ausubo wood, the dense tropical hardwood known scientifically as Manilkara bidentata, were installed in 1792, adding a local material to the imported design. For three centuries, the complex served as both convent and church, a center of Dominican religious life in the colony.

The building's institutional history reads like a relay race. The Dominican Order held the complex until 1836, when the convent was closed and secularized -- part of the broader suppression of religious orders that swept the Spanish empire in the 19th century. The Jesuits took over the church in 1858 and renamed it after Saint Joseph, giving it the name it carries today. From 1911 to 1969, the Missionary Society of Saint Paul the Apostle -- the Paulist Fathers -- managed the parish. But by the 1960s, the congregation had dwindled. People were leaving the San Juan Islet for newer neighborhoods on the mainland, and the old church lost the community that sustained it. In 1969, management transferred to the Archdiocese of San Juan. The convent building took its own path: acquired by the government, it became the Galeria Nacional of the Instituto de Cultura Puertorriquena in 1960, housing Puerto Rico's national art collection in the same halls where Dominican friars once walked.

By the early 2000s, San Jose Church was in serious trouble. The roof was uncertain, the structure was deteriorating, and the building was closed to the public. In 2004, the World Monuments Fund placed it on its Watch list, drawing international attention to the conservation effort. In 2013, the National Trust for Historic Preservation added it to its list of America's 11 Most Endangered Historic Places. Architect Jose Garcia Gomez and engineer Jose Luis Capacete led the restoration, which aimed to revert the design to its original Isabelline Gothic appearance. The work was slow, meticulous, and repeatedly interrupted. During excavation, workers discovered not only the Igneri artifacts but also an obscured arcade, the original location of the pulpit, and a 16th-century sword -- each find adding to the archaeological record while complicating the construction timeline. Hurricane Maria struck in 2017, causing further delays. The COVID-19 pandemic paused work again in 2020.

San Jose Church finally reopened on March 21, 2021 -- two decades after it had closed. The restoration stripped away later additions to reveal the Isabelline Gothic bones beneath, and visitors can now see the ribbed vaulting and stone arches much as 16th-century worshippers would have experienced them. The church sits on a plaza in Old San Juan's historic district, surrounded by the dense colonial fabric of the neighborhood. It is a building that has been a Dominican convent, a Jesuit parish, a Paulist church, a government-adjacent ruin, and an archaeological site. It has survived earthquakes, hurricanes, institutional neglect, and population flight. That it still stands is partly a matter of engineering -- those Gothic vaults proved remarkably durable -- and partly a matter of will, from the architects and conservators who refused to let it collapse. What the Igneri artifacts beneath its floor suggest is that this hilltop has been drawing people for far longer than any one building, any one faith, or any one empire.