Unhealthy eating behaviors and low levels of physical activity are major problems in adolescents and young adults in vocational education. To develop effective intervention programs, more research is needed to understand how different types of motivation contribute to health behaviors. In the present study, Self-Determination Theory is used to examine how motivation contributes to dietary and physical activity behaviors in vocational students. This cross-sectional study included 809 students (mean age 17.8 ± 1.9 years) attending vocational education in the Netherlands. Linear multilevel regression analyses were used to investigate the association between types of motivation and dietary and physical activity behaviors. Amotivation was negatively associated with breakfast frequency and positively associated with diet soda consumption and high-calorie between-meal snacks. A positive association was found between autonomous motivation and water intake, breakfast frequency, fruit intake, and moderate-to-vigorous physical activity. Autonomous motivation was negatively associated with the consumption of unhealthy products. Controlled motivation was not associated with physical activity or dietary behaviors. Different types of motivation seem to explain either healthy or unhealthy dietary behaviors in vocational students. Autonomous motivation, in particular, was shown to be associated with healthy behaviors and could therefore be a valuable intervention target.