Modern dietary habits pose large threats to the global vision for a sustainable food system transition, intensifying discussions around the urgency for educational initiatives that can promote more sustainable food consumption practices. However, research has not sufficiently studied food consumers' moral background, despite its strong influence on food choices, while relevant research on school-aged consumers is even scarcer. This study focuses on two individual ethical decision-making processes regarding food sustainability: moral judgments and moral motives. Data was selected using non-probability, opportunity sampling from 587 students attending the last two grades of primary school in the Region of Western Macedonia, Greece. Participants completed a Likert-scale questionnaire, which adopted a holistic approach towards food sustainability, incorporating the following 12 variables associated with all three domains of sustainability (environmental, societal, economic): Biodiversity, Carbon footprint, Soil, water and air conservation, (Food) loss and waste, Water footprint, Nutrition and health, Animal welfare, Workers' rights and safety, Cultural traditions, Food supply, Tax revenues and Profits, Jobs/incomes. In the moral motives scale, additional variables associated with non-moral considerations were also assessed: Sensory Appeal, Mood, Promotion, Social influence, Convenience and Familiarity. For the moral judgments scale, findings revealed low to medium scores for all the domains and among the variables associated with a sustainable food system, the lowest mean scores being recorded in those linked to the social dimension of sustainability. Regarding food consumption motives, results indicate that non-moral considerations prevail remarkably over moral ones and are linked to all three domains of sustainability. Statistical testing identified grade level, gender, place of residence and participation in environmental, health or food education school programs as factors influencing certain aspects of students’ moral thinking at a statistically significant level. Insights gained from this study can contribute to educational and other agendas aiming to promote sustainable food consumption.