Much as its predecessor, Warrior Within is a 3D platformer centered on exploration and melee combat. As in the prequel, the level design revolves around navigating treacherous environments with parkour and freerunning-styled moves. Unlike Sands of Time, the game world is highly nonlinear; the player would often return to already visited locations several times from various directions, often traversing time portals to visit the same places in the present and the past in order to find ways around obstacles which would be impassable in either time alone. Secret areas can be found and explored to gain additional health points and unique weapons, which culminates in discovering a weapon capable of inflicting damage on the Dahaka, unlocking the game's canonical ending. In addition to normal platforming, the game also features episodes where the Prince is chased by the Dahaka and must quickly navigate trap-ridden hallways to reach safety. The game's atmosphere has a distinctive darker and grittier theme, in contrast to the colorful palette of the previous game.
The combat system has undergone a revision and allows the player to wield an additional secondary weapon in addition to the primary weapon after obtaining weapons either from fallen enemies or weapon racks. With this added feature, this new combat system emphasizes a free-flow fighting style. The idea is to use the environment, secondary weapons and the Prince's own acrobatic abilities to dispatch enemies with ease and aggression, complete with graphic violence effects that can be toggled in the in-game options menu. Two-hand fighting introduces numerous additional acrobatic combos to dispatch enemies with greater efficiency and brutality. Off-hand weapons have varying bonuses and penalties applied to the player's damage and hit points; they can be thrown at enemies to allow a limited form of ranged combat. Most also have limited durability and become unusable after a number of hits, or after they are thrown as projectiles. Aside from bosses, the enemies are sand creatures of varying sizes. Unlike the Sands of Time, where rounds of heavy combat are interspersed with rounds of exploration, enemies can be encountered anywhere along the way, alone and in packs; some common enemies would respawn as the player revisits locations.
As in Sands of Time, the Prince possesses a limited control of time with his Medallion of Time; the Sands can be used for more efficient combat as well as to slow down and even rewind time, allowing the Prince to retry ill-timed jumps or escape Dahaka's clutches.
