The gameplay involves exploring a top-down world map to access different locations or scenarios. During battles, the characters are shown from a top-down or third-person perspective, with movement based on grids. Characters have various offensive and defensive actions available based on their class, including melee, guard, ranger attacks, and spells. The player must also take into account obstacles in the environment and the linking system, which determines who can act out of turn.
The game features a unique magic system based on Pluton, a rare substance shared among party members. Due to its scarcity, it can only be used sparingly. Natural Doctrine supports single-player mode, as well as competitive and cooperative online multiplayer games, where players collect and build decks of cards to strengthen their team over time.