During the development of Rhythm Heaven Megamix, series composer Tsunku was diagnosed with laryngeal cancer and had his vocal cords removed as part of his treatment, impacting both his work and mental health. Despite this drastic health setback, Nintendo remained committed to continuing the game's development with him, which he cited as one of the "beacons of hope" that enabled him to push through his recovery. Around the same time, Nintendo's then-CEO Satoru Iwata had also been battling bile duct cancer, and died one month after the game's release. Since then, Tsunku had occasionally received offers from other companies to make games that were similar to Rhythm Heaven, but declined them under the belief he would get to work with Nintendo again on a new entry, as he had received many requests for it from fans through social media and directly to his office. Tsunku felt that it was his way of showing indebtedness to Nintendo for their support over the years, and he would later return to create the music for Rhythm Heaven Groove.

The last two sets of challenges in Paprika World in Challenge Land are named "Wario... Where?" and substitute the Rhythm Heaven characters for guest appearances by characters from the WarioWare series, a nod to how both series share the same artist and character designer Ko Takeuchi.