At early ages (6–12 years), the levels of physical activity developed in sports initiation and Physical Education often fall short of optimal levels. Ecological models of education seek, among other things, to make up for this deficit by modifying the structural elements of sport, bringing play closer to the child’s developmental characteristics. In this sense, Nonlinear Pedagogy is a model of active pedagogy that seeks the integral development of young players through a sport more in line with their abilities, and that for this is based on a system of constraints on the environment, the task and the player himself. However, there are no studies that analyze the effects of these methodologies on the parameters of physical activity at such an early age. The aim of this study was to analyze the impact of a learning methodology based on Nonlinear Pedagogy on health-related levels of physical activity (heart rate) in young football players (U-11). A quasi-experimental study was developed in which three tasks were applied using structural modifications of the football elements related to Nonlinear Pedagogy (modification of the number of players related to situations of inferiority, equality and numerical superiority; dimensions of the field of play). The sample studied was composed of football players, U-11 n = 32), age: 10.35 ± 0.54 years; years of experience: 2.14 ± 0.768 years. The players carried out each task for 10 min. Physical activity levels were measured by controlling heart rate using heart rate monitors (Polar Team2). The results showed very high levels of vigorous and very vigorous physical activity in all the tasks designed. These data show that the use of these new teaching methodologies has an impact on levels of physical activity in accordance with the recommended parameters.