Unhealthy eating behaviors and low levels of physical activity are a major problem 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 the 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 type of motivation and dietary and physical activity behaviors. Amotivation was negatively associated with breakfast frequency and was 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. Type of motivation seems to partly explain dietary and physical activity behaviors in vocational students. Autonomous motivation in particular was shown to be associated with healthy behaviors and could therefore be a valuable intervention target.