Battle Magnus can only be used in battle. Outside of battle, the player assembles a deck of Magnus for each party member, from which he or she draws random hands. Hand size, deck size and maximum combo size go up as the player upgrades the party members' Class by finding character-specific Magnus and having them applied at the Church. However, as the character's class go up, they are also given less time to choose their initial magnus during each turn. At the highest class level, for example, only five seconds are given to choose the first magnus, and the character misses their turn if they do not choose one in time. Weapon cards are used to fight with, Armor cards to block with, and Effect cards cause a variety of things (food cards, for instance, heal HP and can be applied to both allies and enemies).

Each Magnus has a Spirit Number in the corner ranging from 1-9. As the game progresses the player will encounter Battle Magnus with more than one Spirit Number (up to four). The Spirit Numbers are utilized during battle in order to create straights and same-number groupings (pairs, three-of-a-kinds, etc), thus resulting in an increased effect. On cards with multiple spirit numbers, the player can select which number they want to use with the C-stick. Battle Magnus are removed from the active deck in the course of a battle until A) the character runs out of cards in his/her deck and loses a turn in order to reshuffle or B) the battle ends. In this manner, Battle Magnus are replenishible, as opposed to Camp Magnus.

Finishing moves are a special type of attack magnus. They have some restrictions on their use: they can only be played after a certain number of magnus have been played in a combo, and they immediately end a combo even if it has not yet reached maximum size. However, they are very powerful and visually impressive. Finishing moves are character-specific, and each playable character can collect nine of them throughout the game. All bosses and most enemies use finishing moves as well.

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