These hills consist of Late Pliocene to Early Pleistocene, thin to medium bedded, sandy to rubbly marine limestone.

[9][10] These conical hills are geomorphological features called cockpit karst, which were created by a combination of the dissolution of limestone by rainfall, surface water, and groundwater, and their subaerial erosion by streams after they had been uplifted above sea level and fractured by tectonic processes.

[11][12][13] The origin for the conical karst of the Chocolate Hills is described in popular terms on the bronze plaque at the viewing deck in Carmen, Bohol.

They include sub-oceanic volcanism; limestone covered blocks created by the destruction of an active volcano in a cataclysmic eruption;[16] and tidal movements.

The theories involving either a sudden, massive geologic shift, coral reefs being erupted from the sea, or tidal movements lack any corroborating evidence and support among geologists.

[22] Land-use conflict prompted President Gloria Macapagal-Arroyo to sign an amendment to Proclamation 468 dated September 26, 1994, declaring the land around or in between Chocolate Hills as no longer part of the national monument during the Sandugo celebration on July 17, 2002.

This amendment allowed the tracts of land surrounding and within the famous tourist spot to be developed by the provincial government and other entities that have control over the area.

01147 entitled "an act declaring the Chocolate Hills as national patrimony and geological monuments, penalizing their plunder, destruction or defacement, and for other purposes."

Before they were designated national geological monuments, some of the hills (about 310,455 ha (1,200 sq miles)) were classified as alienable and disposable[26] or private lands such that they were titled to some locals.

The declaration consequently caused some social unrest, resulting in almost simultaneous civil uprising, led by the long-established New People's Army (generally described as Maoist guerrillas) establishing a new front, known as the Chocolate Hills Command.

[12] Meanwhile, the provincial government has suggested that the legislation defining the Natural Monument should be changed, which will require that the proclamation be redrafted and ratified by both the Philippine House and Senate.

[12] Future development and investment challenges within the Chocolate Hills area include: obtaining the national government's sanction for the project; persuading landowners to sell; convincing the Protected Areas Management Board, which has jurisdiction over the hills, not to use its veto power over any investment requiring physical facilities.

[29] In response, Congress launched inquiries which led to the resort being built despite the hills' protected status and the subsequent six-month suspension of 68 local officials including Bohol governor Erico Aristotle Aumentado.

[33] In October 2018, the Provincial Development Council’s (PDC) Executive Committee proposed ₱200 million in funding for the repair work, and restored the viewing deck and the surrounding facilities, including the pathways, parking space, water features, trellis, stairs, ramps, food court, museum, activity center, lamp posts, signages and landscaping works.

During a rainy day when the ground became muddy, a hostile encounter between them prompted the worried people to vacate to other parts of the island, and the giant from the north instigated a mud throwing fight.