Research on the impact of the Sport Education model (SEM) in motivational terms is prolific and consistent; however, studies that jointly address the effects of the SEM on adolescents’ motivational, emotional, and well-being dimensions are scarce. This study aimed to examine the effect of a multi-season SEM-based program on self-determined motivation, basic psychological needs, emotional intelligence, satisfaction with life, and the intention to be physically active on physical education (PE) students during a school year. A total of 212 high school students ( M  =  13.88; SD  =  1.68) from grades 7 and 10 (nine intact groups) participated in this study. A quasi-experimental design, with four measurements (T1, September; T2, December; T3, March; and T4, June), without a control group was carried out. The repeated measures analysis of variance, with time as within-subject factor, and both grade level and gender as between-subject factors, revealed significant effects over time on autonomy F(3, 624)  =  12.413, p < 0.001, η2  =  0.056, competence F(2.78, 579.09)  =  10.733, p < 0.001, η2  =  0.049, emotional control and regulation F(2.74, 569.74)  =  7.045, p < 0.001, η2  =  0.033, and emotional empathy F(2.71, 563.71)  =  4.248, p < 0.01, η2  =  0.007. Some interactions were also found according to grade level and gender. Between-subject multivariate analysis of variance (MANOVA) showed differences tended to progressively increase over time. Results confirm the potential of the SEM to cushion motivational decline and satisfy the basic psychological needs during adolescence. Furthermore, the SEM was shown to be a useful approach for increasing the emotional intelligence dimensions in the PE context.