Yoshi was originally planned to appear in Super Mario Galaxy, and was featured in proposal documents for the game from 2005. However, he was removed due to the developers thinking that "it would've been too much all at once." They said that, "if you're going to put Yoshi in a game, he has to be a main element, but [Super Mario Galaxy] had spherical land forms and gravity shifts and lots of elements that were entirely new" and, "Even if we had used him, we might have only been able to use him on a single stage."

Despite this, it was decided early on in the development of Super Mario Galaxy 2 to include Yoshi in the game, because his control scheme could act as a new main element of a new game and a "multiplication" of the elements from the previous game. The Wiimote controls for Yoshi were also formed early in development, with Shigeru Miyamoto taking pride in the tongue pulling mechanic used for eating fruit, fighting enemies and flipping switches, saying it "isn’t like anything you've ever experienced before." The rest of Yoshi's controls were shaped based on internal feedback from "everybody's love" for Yoshi, listing the development team, Mario Club Inc., and Nintendo of America as primary influencers for what the image of Yoshi should be, but tried to avoid making him too powerful. The developers also had composer Kazumi Totaka record new voice lines for Yoshi for the first time in ten years, and was reported as feeling "a little uneasy" and worried that Yoshi would sound like he had aged, but these were not concerns to them and the recordings were used in the game.