In a post-release interview with Game Informer, AlphaDream producer Yoshihiko Maekawa and Nintendo producer Akira Otani stated that the decision to develop the game for the Nintendo 3DS (then in its twilight as an incumbent platform) instead of the Nintendo Switch was due to the former allowing the developers to carry over the original game's dual-screen gameplay, as well as due to timing where they could build off existing assets. They also cited numerous factors behind AlphaDream's decision to remake the third game in the sub-series directly after the first game (thus skipping the second game, Mario & Luigi: Partners in Time). According to Otani and AlphaDream director Shunsuke Kobayashi, the biggest factor was that Bowser's Inside Story was "the best received title in the series", with other reasons including a desire to explore the father-son relationship between Bowser and Bowser Jr. in Bowser Jr.'s Journey and the ability to carry on Fawful's subplot from the Bowser's Minions mode in Mario & Luigi: Superstar Saga + Bowser's Minions. Kobayashi described the process of developing the new mode as "really fun for us" thanks to the ability to emphasize the comedic aspects of the game's cast, with Otani further highlighting the opportunity to tell a kid-friendly story about a protagonist rebounding from hitting rock bottom.

In an interview with Nintendo Dream, it was revealed that the Best Fitness Friends (the main antagonists of the "Bowser Jr.'s Journey" side mode) used to work for the game's main antagonist Fawful alongside Midbus. By the events of the game, however, they have largely distanced themselves from Fawful, instead running a shop that sells a variety of things. Additionally, it was revealed that they are actually members of the same race as Midbus (hence why they have the same skin color as him), but their relationship with him has soured.