This longitudinal study aims to examine how changes in health behaviors and socio-cognitive factors influence the academic achievement of Lebanese adolescents over a period of 12 months. Adolescents (n = 563) from private and public schools in Mount Lebanon and the Beirut area, aged between 15 and 18, participated in a three-wave longitudinal study and completed a self-administered questionnaire assessing socio-demographics, health behaviors, socio-cognitive factors, parenting styles, and academic achievement. A linear mixed model was carried out to examine if changes in health behaviors and cognitive factors affect changes in academic achievement after 6 and 12 months from the baseline, adjusting for demographic variables and parenting style. Results show that improved adherence to the Mediterranean diet and an increase in self-efficacy were associated with an increase in academic achievement. An increase in adherence to the Mediterranean diet had the same effect on academic achievement 6 and 12 months from the baseline, whereas an increase in efficacy beliefs was only significantly associated with achievement at 12 months from the baseline. This study supports the longitudinal link between diet quality and efficacy beliefs with the academic achievement of adolescents. This relationship is independent of sex, age, religion, parents’ education, and raising styles.