PE teachers’ motivational styles have a substantial impact on students’ engagement in learning and can influence children to adopt physically active lifestyles. The Self-Determination Theory (SDT) seeks to explain human motivation and behaviour. Central to SDT, three basic psychological needs must be supported (the needs for autonomy, competency and relatedness) to enhance intrinsic motivation. Autonomy-support refers to the subjective experience of autonomy. Structure is important in PE as it creates the conditions whereby effective learning can take place. The current study examined the effects of a ten-week, school-based, autonomy-supportive structure (ASTS-PE) teacher training intervention in PE, on students’ PE outcomes. Psychological needs satisfaction, perceived autonomy-support, relative autonomy index (RAI), engagement and objective moderate-vigorous physical activity (MVPA) levels in PE were measured. The study consists of two treatment (autonomy-supportive structure and autonomy-support only) and one control group. The results indicate that students in the autonomy-supportive structure group show better overall outcomes compared to the other two groups. The findings in this study provide strong evidence that both autonomy-support and structure are needed to maximise effectiveness in PE lessons. We further suggest practical ways in which teachers could implement an autonomy-supportive structure in their lessons.