Included among the basic objectives of Physical Education (PE) classes is the consolidation of habits of a healthy lifestyle among adolescents. However, the main studies in this field have focused on cognitive aspects related to students during these classes, yet they ignore the role that emotions can play in the adoption of future habits. Objectives: To analyze how emotions (emotional intelligence and emotional state) can influence the resilience and motivation of adolescents, as well as academic performance and adoption of healthy lifestyle habits. Methodology: 615 secondary school students between the ages of 14 and 19 participated (M = 16.02; SD = 1.57) in the study. A structural equations model was developed using the main variables and by applying some of the principles of Self-Determination Theory. The results show that emotional intelligence is positively related to positive emotions and negatively related to negative emotions. Positive emotions positively predict both self-motivation towards physical education classes and resilience. Resilience positively predicts self-motivation. Finally, self-motivation acts as a predictor of both academic performance and regular participation in physical activity. Conclusions: This study successfully shows the importance of focusing on emotions in PE classes inasmuch as emotion increases the tendency to get good grades and maintain active lifestyle habits. In this sense, focusing on the emotions of students in PE could prove quite beneficial.