Onimusha: Way of the Sword provides players with multiple avenues for character customisation and progression beyond its main narrative. The game features cosmetic sword skins that allow protagonist Musashi to alter his weapon's appearance without affecting combat effectiveness, alongside environmental puzzle mechanics such as the mask-sequence challenge at Nijo-jo Castle, which requires players to strike targets in a specific sequence to unlock progression gates.

The title emphasises optional content through dedicated side missions and collectibles. "Ace Archer" quests appear across multiple locations—including Nijo-jo Castle and Kyoto Imperial Palace—wherein players hunt flying aerial enemies using ranged combat. A network of hidden treasures distributed throughout the explorable Kyoto setting triggers additional optional missions once players reach the "To Live is to Suffer" checkpoint in the main story, rewarding thorough exploration and completionism.