According to an interview with Mitsuru Kamiyama who directed Final Fantasy Crystal Chronicles: Ring of Fates, he came up with the idea two weeks before the original Crystal Chronicles game was completed. When he came up with the idea he wrote it all down on a chopsticks wrapper, showed it to the Executive Producer, and was given the thumbs up and was added to the final game. The feature was popular, and was added into the next game.
In single-player mode of Crystal Chronicles, players could paint the moogle Mog who carries the Crystal Chalice for them. Whenever the player enters a Moogle's home, Mog can be found in front of the fire place and there he will ask the player if they want to paint him. He can only be painted with three colors: red, blue, and green. Depending on what he was colored, each paint would give Mog the ability to cast certain spells, and changes what data is displayed on the Game Boy Advance if the player plugs it in.
- White - Fire, Blizzard, or Thunder randomly. Map on GBA.
- Red - Fire. Treasure Radar on GBA.
- Blue - Blizzard. Scouter on GBA.
- Green - Thunder. Monster Radar on GBA.
In Ring of Fates story-mode, players could once again paint a moogle. The moogle can usually be found near a Save Point. After giving the player a Moogle Stamp he will ask if they would like to paint him. Due to the touch screen, Moogle Paint has much more options then the original games version.
Players can change the moogle's pompom, fur, ear, foot, and wing color. The moogle's face, head, and body can be painted on. Mog Trader allows players to send or receive painted moogles from other players via Wi-Fi.
A contest was held on the Japanese and North American Final Fantasy Crystal Chronicles News blog, where players could send their painted moogle in via Wi-Fi to win a prize.