Currently, there are several methodological models that have broken into different disciplines of knowledge with the aim of making the teaching/learning process more dynamic, active and participatory for students. This is the case of Flipped Classroom, which is based on a mixed approach between e-learning and face-to-face teaching, as well as gamification, which bases its didactic principles on the recreational components of the games. Within this context, the aim of this research is to observe what effect the application of Flipped Classroom and gamification has in the development of motivation, autonomy and self-regulation towards learning through a didactic unit on healthy habits and diet in 202 students of 6th grade of Primary School from four different schools (public and state-subsidized) in the city of Granada (Spain). For this purpose, a methodological design was used with pre-test and post-test to check the effects of the experience on the students. The findings obtained showed that the application of these methods promoted an increase in students’ motivation, as well as in their autonomy and self-regulation when facing the contents of the subject. For this reason, it is advocated that there is a need to continue promoting a quality and innovative educational practice according to the figure of the student today.