This study aimed to capture the multidimensionality of adolescents' motivation in the physical education (PE) setting, within self-determination theory, by employing self-organizing maps (SOM) analysis. Particularly, it examined the topological relationships among students' basic psychological needs satisfaction, their perception of more or less self-determined motivation and the affective and behavioural consequences in PE lessons across several sociodemographic variables. A nationally representative sample of 3029 Spanish students (51% girls), aged 12 to 18 years, was surveyed. SOM mapped well-defined students' profiles that embraced interrelatedly a considerable number of students' motivational characteristics. Four target profiles, out of 10, were explored. The first two profiles, highly motivated to be active girls and boys, mainly experienced senses of self-determination, but also controlled reasons for participating in PE lessons, high perceived competence, relatedness and autonomy fulfilment, perceived exerted effort and satisfaction. However, the reluctance to be physically active presented two gendered motivational profiles. Barely motivated to be active girls showed the lowest levels of self-determined motivation, including introjected regulation, low perceptions of competence, autonomy, relatedness, and dissatisfaction in PE. Vaguely motivated to be active boys revealed that despite their perceptions of competence the neglect of the other two psychological needs was more likely to determine a controlled motivation and, consequently, maladaptive outcomes. SOM proved to be a more robust and accurate clustering technique than the k-means algorithm and helped to portray and visualize the complexity behind the decision to become an active person considering the motivational processes in PE. Implications are provided for practitioners.