In an attempt to conquer the world, the Nuisance World has stolen the Majoka Jewels and have corrupted each into an Akiramestone, which interferes with people's dreams and turns them into an Akiramest. Momoka, an ordinary middle school student, is summoned by Mokonyan, a fairy from the Magic World, to join Magic Warriors Rin and Mitsuki and stop the Nuisance World. Together, as MagiMajo Pures, they purelize the Akiramests back into Majoka Jewels with magic.

The Music Kingdom contains musical treasures called Sound Jewels, which together produce the "Song of Blessings." The Sound Jewels are stolen by Maou, who corrupts them into Negative Jewels. Through the Dokudoku-dan, the Negative Jewels are used to turn humans into Negative Jewelers to spread a Negative Aura for Maou to use in his plan to conquer the human world by composing an evil song. In order to recover the Sound Jewels, the goddess of the Music Kingdom sends the Fairy Rhythms; Poppun, Rocky, and Kuranosuke, to the human world to seek help.

The story revolves around the Music Kingdom, a land that contains musical treasures called Sound Jewels, which together produce the “Song of Blessings”. The Sound Jewels are stolen by the Demon King, who corrupts them into Negative Jewels. Through the Dokudoku-dan, the Negative Jewels are used to turn humans into Negative Jewelers to spread a Negative Aura for the Demon King to use in his plan to conquer the human world by composing an evil song. In order to recover the Sound Jewels, the goddess of the Music Kingdom sends the Fairy Rhythms Poppun, Rockie, and Clanosuke to the human world to seek help.