Way of the Samurai 3 follows the same principles as its predecessors, offering an authentic setting, a deep sword-fighting system, and cause-and-effect role-playing. The game takes place during the Sengoku Period and puts the player in the sandals of a lone samurai who is the only survivor of an epic battle. This sets him on a path to decide whether to join Fujimori Clan, Ouka Clan, protect the villagers in Takatana or leave Amana for good, which would result in a complete game reset.
The player's choices and actions throughout the game greatly impact the story arc, with over 20 possible endings. The length of the game varies depending on what the player does, with the shortest playthrough being around an hour long. The player has three options to interact with NPCs: listen, apologise/beg or attack.
The game features a realistic day and night cycle, which affects the NPCs' behavior even when the player isn't interacting with them. Decisions made by the player influence their relationships with different groups, changing how they interact with the player. The player can choose from dozens of swords, hammers, and spears to defend themselves, each with its own variable quality and durability level.
The player can also decide whether to kill someone or fight them with a blunt weapon, affecting their reputation and future interactions. They can craft new weapons by forging them out of spare parts or enhance existing ones according to their fighting style. During the game, the player may meet several possible partners, some of whom will join them for money, while others can be "romanced".
Partners can provide an additional edge in combat and unlock access to mini-games and side jobs with two players. Romance options even allow the partner to decide whether to live with the player in Takatane village, where they have access to a safe and closet for storing items.