Several studies have shown that following a healthy diet and practicing regular physical activity (PA) are related with multiple health benefits. However, the cognitive and academic implications of these behaviors within adolescents requires further study. A cross-sectional study was conducted with a simple of 1059 adolescents from Spain. The main instruments employed were the Adherence to Mediterranean Diet Test (KIDMED), the Physical Activity Questionnaire for Adolescents (PAQ-A) and the Motivation and Learning Strategies Short Form (MSLQ-SF). Practicing PA for more than three hours per week was related to better dietary habits ( < 0.001) such as increased consumption of vegetables (0.75 ± 0.43 vs. 0.62 ± 0.48), fish (0.67 ± 0.47 vs. 0.58 ± 0.49), cereals (0.85 ± 0.35 vs. 0.77 ± 0.41) and nuts (0.44 ± 0.49 vs. 0.35 ± 0.47). High adherence to a Mediterranean diet (MD) was positively related to elaboration strategies ( = 0.116), organizational strategies ( = 0.109), critical thinking ( = 0.116), self-regulation ( = 0.159), time and study habits ( = 0.160), self-regulation of effort ( = 0.118), and intrinsically orientated goals ( = 0.090) ( < 0.01 for all variables). Practicing PA every week was also related to improvements in several of the measured variables and in addition was related to lower levels of anxiety within the academic environment ( = -0.070; < 0.05). Given the benefits of eating habits and the practice of PA in the cognitive processes involved in adolescent learning, intervention programs within the educational context are recommended to improve healthy habits.