Monolith Soft was originally owned by Namco, but their relationship took a negative turn after Masaya Nakamura stepped down as president of Namco in 2002, three years prior to the company's merger with Bandai. As the company underwent changes, Monolith Soft felt that they were being given less creative freedom due to the newly-created Bandai Namco being less willing to take creative risks. They received consultation from Nintendo executive director Shinji Hatano, who advised them to continue making innovative projects. This inspired Monolith Soft to break away from Bandai Namco in favor of becoming a Nintendo subsidiary: Monolith Soft was allowed creative freedom in exchange for developing software exclusively for Nintendo platforms.

Initially, Nintendo had acquired an 80% share of the company, while Bandai Namco retained 16% of the company and remained as a development partner in part to strengthen their relationship with Nintendo. The remaining 4% was divided between the company's founders: Tetsuya Takahashi, Hirohide Sugiura, and Yasuyuki Honne. However, by April 2011, Nintendo had acquired the remaining 400 shares from Bandai Namco, granting them 96% ownership of Monolith Soft. The acquisition as a whole was notable for contrasting Nintendo's previous approach of not taking part in mergers and acquisitions of other companies. In a statement on the matter, former Nintendo president Satoru Iwata stated:


In December 2024, Nintendo purchased the remaining shares from the company's founders, fully acquiring Monolith Soft.