The church is built on the banks of the Loboc River. It has a cruciform plan, with a sunken pyramidal roof on its crossing.
In 1998, Loboc Church was declared a National Historical Landmark by the National Historical Institute. It was also listed as a National Cultural Treasure by the National Museum of the Philippines.When a 7.2 magnitude earthquake struck Bohol and other parts of Central Visayas on October 15, 2013, its severe damage made restoration difficult. In 2017, an effort to faithfully restore it began. On May 16 2021, the church was finally reopened after years of restoration efforts.