Standard video games are applications whose development process often follows a traditional software methodology. Serious Games (SGs) are a tool with an immensely positive impact and great success. SGs enable learning and provide entertainment and self-empowerment, which motivates students. The development of an SG consists of complex processes requiring multi-disciplinary knowledge in multiple domains, including knowing the learning domain and adding the appropriate game mechanics to foster high intrinsic motivation and positive player experience that makes the players feel like they are having fun while learning. Otherwise, the game is viewed as boring and not as a fun and engaging activity. Nevertheless, despite their potential, the application of SGs in education has been limited in terms of pedagogy. Several authors assert that this lack is because SG standards and guidelines have not been developed. There is an imbalance between experts’ contributions to education and game design specialists for the SG development. Not all the SGs that have been developed have applied appropriate design methodologies that incorporate both the entertainment mechanics and the serious component. To ensure that an SG meets the user’s expectations, it must be designed using an appropriate method. This work aims to present iPlus, a methodology for designing SGs based on a participatory, flexible, and user-centered approach. Additionally, this paper analyses several case studies with the iPlus methodology.