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 song "Love Me Forever!", which plays during Remix 8 of the game, is sung by Japanese singer Ado and written especially for her by Tsunku. According to Tsunku, the idea of collaborating with Ado first came about after hearing her cover of the song "Mecha Mote I LOVE YOU". Tsunku spent nearly a year trying to come up with a song that was "quintessentially Rhythm Heaven and right for Ado to sing", before finally coming up with an idea after watching Ado perform live in Hawaii. Notably, if the player holds the A button at the start of Remix 8, the visuals will be changed into silhouettes in reference to Ado's concerts.

Various characters from the WarioWare series make cameos throughout Rhythm Heaven Groove:

• At the start of Sneezy Moon, Ashley has a chance of appearing amongst the swarm of bats, using her design from Game & Wario. This is hinted at by the "Magician in the Night" Info Tidbit.
• During Soccer Dreams 2, Mona has a chance of appearing on the bench behind Sora, wearing her cheerleader outfit from WarioWare: Smooth Moves. Similar to Ashley's cameo, this is hinted at by the "Benchwarmers" Info Tidbit.
• In the Try Again epilogue of Synchro Wings 2, the Alien Bunnies appear piloting the UFO that the Migrating Birds are resting on.
• In the Good epilogue of Pet N Parcel 2, one of the Sasquatch Family members from WarioWare Gold is shown accepting the package from the rabbit.