Ben 10: Protector of Earth is a game where the player controls Ben and helps him to travel into 5 regions from the United States in order to recover all the Omnitrix's DNA samples stolen by Vilgax, which want use it to destroy the world. Its levels consist of solving puzzles, along with enemy waves where the player needs to fight to continue. He also has the access to the Omnitrix, which permits Ben to transform into different alien forms with specific abilities that can be used for combat, puzzles, etc.

In the beginning, Ben is only able to access a few of his alien forms for a limited time, but after defeating some bosses, Ben can eventually access five of his ten forms (Four Arms, Heatblast, XLR8, Cannonbolt and Wildvine) and even unlocks the master control, meaning he can stay alien for an infinite amount of time or switch between aliens without draining Omnitrix energy. Attack combos can be unlocked by collecting Omnitrix points. Limited power boosts or invincibility can be gathered, as well as bonuses to make the Omnitrix recharge faster. Three Sumo Slammer cards are hidden in each main level, and once collected unlock features, such as movie clips.

After each level, Plumber ranks are rewarded, depending on how fast the player beats that level. If the player gets an A rank, you get a character view, usually a boss or a villain. In the main boss levels, a quick time event allows players to execute a special attack at certain points.