Given the low motivation and engagements of some students during the Physical Education (PE) lessons, the main aim of this study is to analyze the relationship between the learning methods adopted by teachers (constructive, productive, reproductive, and laissez-faire) from the students’ perspective, and the motivational processes and the engagement of the students during the PE lessons. Participants were 465 male (n = 223) and female students (n = 242) aged between 10 and 14 years-old (M = 11.36; SD = 0.91) belonged to Elementary Education (fifth and sixth grade, n = 293) and Secondary Education (first and second grade, n = 172). Through a study with a correlational and cross-sectional design, students fulfillment self-reported questionnaires about teaching-learning methodologies, motivation and engagement. A structural equation modelling was used. The results showed that the constructive and reproductive methodologies were associated with the autonomous motivation. In addition, the productive and reproductive methodologies were related to the controlled motivation, whereas the productive methodology were associated with the amotivation. Finally, only the autonomous motivation was significant related to the engagement for PE lessons. Therefore, due to these obtained results, PE teachers should select more student-centered methodologies instead of teacher-centered methodologies, with the aim to get a higher quality student-motivation and engagement in the development of PE lessons.