Like the previous Pokémon Trozei game, Pokémon Battle Trozei includes a multiplayer mode. This mode is local multiplayer only and requires all 2 to 4 players to have a 3DS console and a copy of Pokémon Battle Trozei or Pokémon Link Battle. This game is not region locked, so play can work between any region of game.

Once multiplayer is selected, one player should select "Form a Team" while the other players should select Join Team. The player who selected to create it will have the full control. Once all players are activated and joined, you have the ability to change the Support Pokémon while the lead player can select the level. The levels selectable are not restricted in any way and are the same levels as in the single player. Once selected, the gameplay begins

The gameplay in multiplayer is largely the same as single player. Each player will run their own Trozei box, which is different to each other players. As each player begins a combo, it will show up on the other player's top screen, with the Pokémon you're using and the number your combo is currently at. When the combo ends, your attack will go through. The Pokémon you are battling is the same on all games and each player's attacks are factored in. When each player has ended their current combo after the Pokémon has the OK symbol denoting it's ready for capture, it will be captured

When all Pokémon are captured, the scores are tallied. The overall score is a result of all players added together and all players capture the Pokémon in question. In addition to this, on the bottom screen, all players are ranked based upon their contribution to the score.