The church was declared a National Cultural Treasure by the National Museum of the Philippines and a National Historical Landmark by the National Historical Commission of the Philippines. Together with the churches of Maragondon, Loboc and Guiuan, the Baclayon Church was formerly included for the UNESCO World Heritage Tentative List of the Philippines since 1993 under the collective group of "Jesuit Churches of the Philippines". When a 7.2 magnitude earthquake struck Bohol and other parts of Central Visayas in 2013, the church building sustained major damage. Reconstruction by the National Museum of the Philippines started in 2013, and was completed in 2017