Background: The implementation of a quality daily physical activity program in school is influenced by a multitude of factors. Considering the characteristics and possible interactions of factors when choosing the study methods is likely to influence the interpretation of the results. Mixed methods approach, by collecting both quantitative and qualitative data, can lend a more comprehensive understanding of a physical activity intervention and its effects. Purpose: This paper aims to assess the benefits of a daily physical activity program and underline the theoretical and methodological interrelationships of this project based on an ecological approach and using a mixed methods design. Method: A semi-structured interview was used to collect the perceptions of a physical and health education teacher and self-administered questionnaires were used to survey classroom teachers and parents, while the quantification of the benefits of the program on students was based on an attention test, accelerometer measurements and a motor skills evaluation. Results: This mixed methods study provided an opportunity to measure the benefits of a daily physical activity program at the intrapersonal level (students' attention, PA intensity, and motor skills) and compare these results with findings at the interpersonal level (parents' perceptions), and institutional level (PHE teacher and classroom teachers' perceptions). Examining the benefits associated with the daily physical activity program using qualitative and quantitative measurement tools at different levels of the ecological approach enabled the convergence and corroboration of findings but also the elaboration, enhancement, and clarification of findings. Conclusion: A mixed methods design has helped to make an optimal use of the ecological approach despite the presence of methodological limits but has also helped to increase the effectiveness of classroom teachers and physical and health education teacher delivering the daily physical activity program, and ultimately to reap greater benefits.