Natural Doctrine is a tactical, turn-based role-playing game set in a fantasy universe where humans fight other races. The player controls the guard soldier Geoff who works out of the fortress city Feste. Initially, he goes after a number of goblins to gather resources, which starts a large story. The player eventually assembles a party of up to ten different characters with classes such as all-round warrior, apprentice, battle medic, sword specialist, and sword master. Characters carry gear and equipment found through loot and earn experience in battles to level up and improve their abilities.
From a top-down world map, different locations or scenarios are available. During battles, the characters are shown from a top-down or third-person perspective. As a turn-based game, movement is based on grids. Characters have various offensive and defensive actions available based on their class, with melee, guard, ranger attacks, and spells. The position of each character in the grid also matters, as specific actions become available or characters can act out of their turn, called linking.
Magic attacks are based on a substance called Pluton, which is rare and shared between all party members. Because of its scarcity, it can only be used occasionally. The game supports competitive and cooperative online multiplayer games, similar to single-player mode, but with the added challenge of collecting and building a deck of cards that becomes stronger over time. Cross-platform multiplayer and cross-save functionality are available for PlayStation 3.