Eating habits appear to become less healthy once children move into adolescence. Adolescence is characterized by increasing independence and autonomy. Still, parents continue influencing adolescents’ eating habits. This cross-sectional study used a Self-Determination Theory perspective to examine how parents can support preadolescents’ food-related autonomy and competence and how these factors are associated with healthy eating motivation and food consumption at school. In addition, the effect of relative healthy food availability at home on preadolescents’ food consumption at school was explored. In total, 142 Dutch preadolescents (mean age 12.18) and 81 parents completed questionnaires. The results showed that preadolescents perceived themselves as having higher food-related autonomy and lower competence to eat healthily as compared to their parents’ perceptions. A path analysis was conducted to test the hypothesized model. Although parental support was positively associated with food-related autonomy, higher food-related autonomy was related to less healthy food intake at school. On the other hand, competence to eat healthily indirectly affected preadolescents’ healthy intake ratio through their healthy eating motivation. Finally, the relative availability of healthy options at home was positively associated with preadolescents’ healthy intake ratio outside the home. Findings from the study advance the understanding of individual and environmental factors that influence eating habits during the key life period of early adolescence. The results may inform interventions aiming to guide preadolescents to make healthy food choices on their own.