In this article, we will describe the embedded case study of the European project “E-Magic” carried out within the Erasmus+ project and which involved 12-16 years old students and teachers from three nations: “Acharnes Special Education Vocational School” in Athens (Greece), IIS “L. Da Vinci-Nitti”, a high school in Potenza (Italy), and from Gabinete de Modernizao das Tecnologias Educativas (G.M.T.E.) in Madeira Islands (Portugal). The project is finalized to enhance Mathematical Competencies by Serious Games learning. We carried out both empirical qualitative and quantitative methods to highlight Serious Games’ effectiveness, as a teaching methodology, in motivating students to learn mathematics. We also hypothesize that prompting a strategic way of thinking within a didactical intervention by game-approach could improve students’ proving processes and support them in mathematical thinking production. Rabardel’s cognitive ergonomics and the Technological Pedagogical Content Knowledge model are the lenses for reading educational experiments’ data. Data seems to show that simulation helps students find alternative and creative solutions to problems. Therefore, Serious Games’ use in education promotes significant changes and mental resources activation.