The most notable gameplay change is in regards to how you achieve the various combinations in the puzzle. In the original Pokémon Trozei, you would slide the rows horizontally or the columns vertically in order to match the Pokémon. In Pokémon Battle Trozei, however, what you do is pick up a Pokémon and move it, swapping it with its replacement. This completely changes up the way the game is played.

Like before, you need to make matches of three or more Pokémon, and when you start making combos, this will reduce to two in order for maximum efficiency. When you've made combos and Trozei Chance/Link Chance activates, you get several seconds to move Pokémon to continue the combo.

In the previous game, capturing a Pokémon was just as simple as matching several of them, and then that's that. However, in Pokémon Battle Trozei, this is completely changed up. In each level, you will encounter multiple wild Pokémon that will sit above the playfield. Whenever you make a match and start combinations which count towards an attack against the Pokémon. These attacks are also factored in by type compatibility so if you start off matching an Electrike, it will be good against a Pidgeot, but not against a Donphan.

Once the Pokémon's Hit Points are reduced to zero, the Pokémon is captured and you can move on to the next part of the zone. There are also some occasions where you will face up against more than one Pokémon at a time.

As you are now facing off against specific wild Pokémon, using the board as means to obtain attacks, the game would be somewhat unbalanced if there was no incentive so you could take your time. This is where the wild Pokémon comes in. These Pokémon can occasionally attack you. When they do, your health metre, seen on the side of the table, will reduce. If it gets depleted, the game is over. You can regenerate it by matching up Chansey.

The attacks of the Pokémon vary depending upon the Pokémon species, however the power can increase. On the odd occasion, the wild Pokémon will jump into the table, causing you to have less room to match Pokémon. When they're at this point, the damage will increase.