PokéBase - Pokémon Q&A
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You can get Moon Stones by:

  • Walking around with a Pokemon with Pickup. (Four percent chance at levels 41-60, 10% chance at levels 61-100.)
  • Inverse Battle Shop (Given to you by Inver if you get a score of 7-9.)
  • Secret Super Training (Drag Down Hydreigon)
  • Meteor Falls (Northwest side of the areas you enter.)
  • Jagged Pass (Rematch with Expert Shelby)

Hope this helps!


The Pick-up method is very, very effective.
You can also fill your secret base with five trainers that can give you a random stone each day, good way to hoard for less common stones if you're not into super training marathons.