Masuda served as the director for Pokémon Ruby and Sapphire on the Game Boy Advance, marking his formal entry into a directing role for the main series. He oversaw the creation of the Hoenn region and implemented features like Abilities and Natures for Pokémon.

Masuda continued to direct multiple Pokémon games, including Pokémon FireRed and LeafGreen, Pokémon Diamond and Pearl, and Pokémon Black and White. Each game brought unique features and experiences to the series, contributing to its ongoing evolution.