Mega Evolution is one of the defining features of Pokémon Shuffle. In addition to Abilities, it can drastically change gameplay with effects such as clearing out half the board, and replacing other icons with the Pokémon, potentially causing a very large combo. As in the traditional games, certain Pokémon are able to Mega Evolve, but only if the player possesses the respective Mega Stone. Mega Stones can be obtained by clearing the last stage of any area or from various events.

The player may only bring one Mega Evolving Pokémon to a stage (which must be in the first slot on the player's Support Pokémon team). During gameplay, a Mega Gauge on the side of the screen fills up as the player matches icons of that Pokémon. When a the gauge fills, the Pokémon Mega Evolves, and its Mega Power takes over its original Ability. Some Pokémon take longer than others to fill its Mega Gauge.

Some things to note:

  • If the first match in a combo causes a Mega Evolution, the disruption countdown (if any) does not go down
  • On the 3DS version, the Mega Evolution immediately happens, and any match of the Mega Evolving Pokémon after the match causing it will trigger the Mega Power. In the Mobile version, as of the v1.8 update, the behavior is the same. Before the update, there was a small delay before Mega Powers can trigger, about enough for one or two matches to be processed first.
  • Once a Mega Power takes over, it does not have to be the first match in a combo for it to activate. This makes Mega Evolution very powerful, as any match will activate the Mega Power.
  • When a Mega Power activates, the icons in the match don't disappear until the effects are finished (ex. Mega Gengar finishes erasing all its icons on the board). When they do disappear, they ignore anything that could keep it from staying, including Barriers and intersecting matches (meaning that the other match will not activate).
  • Matching a Mega Evolved Pokémon causes that Pokémon to not spawn for a while (approximately 40 icons) in the same combo