Francisco Colín, an early Jesuit historian, listed the town's name as Malabooch and later changed it to Malabohoc.

[6] During the pre-Spanish era, the town's name was Dunggoan, meaning "place of anchorage" and referred to the sheltered bay where sailors used to land and engage in business with the early settlers.

They laid the foundation of the Maribojoc church in 1798 on what was once swampy land, and it was finished in 1816, after 18 years of work.

Earlier, in 1796, the Punta Cruz Watchtower was built as a lookout against marauding pirates.

[7] Maribojoc was severely affected by the magnitude 7.2 earthquake which struck Bohol, suffering 16 fatalities and damage to some 3,700 homes, as well as total destruction of its Catholic church.