From the World Monuments Fund website:
Dominican friars built the church, beginning in 1532, as a temple to the adjoining sanctuary building within Puerto Rico’s walled city of San Juan. The church was designed as a longitudinal temple with side chapels and was located on the highest point of the Isleta of San Juan on a site donated by Juan Ponce de León.
In 1858, the church passed from the Dominican friars to the Jesuit Order and was renamed the Church of San Juan. Under this new leadership, the church was transformed. The interior design, decoration, and furnishings changed significantly to reflect the fashionable neoclassical style. In 1887, the church was again transferred, this time to the Vicentian Fathers (Padres Paules), who redecorated the interior of the church for the third time in the building’s history.
By the mid-20th century, political, technological, and economic factors had taken a toll on the historic church, and its survival was in question.
So I guess I shouldn't be too bitter that the current restoration project, funded by Puerto Rico's National Endowment for the Humanities, prevented me from seeing more. Still, they should have been notified that I was coming, so arrangements could be made. Good thing I'm a forgiving sort.