Background: This study aims to evaluate food waste and menu quality in two canteens (A and B) from a Portuguese public university in order to identify challenges and opportunities to improve the food service. Methods: Food waste included the analysis of two canteens over 5 consecutive days by selective aggregate weighing. A qualitative evaluation of a 5-week menu cycle related to lunches was performed through the Qualitative Evaluation of Menus (AQE-d) method. Results: Both menus have “satisfactory” evaluations and lower adequacy to the dietary guidelines in criteria A, which evaluates general items from the dish, and in criteria B, which evaluates meat, fish and eggs. The calculated mean of food waste in both canteens exceeded the acceptable limit of 10%, except for the vegetarian (7.5%) dish in canteen A. The biggest waste was found in the vegetarian dish (16.8%) in canteen A. In meat dishes the conduit presents more waste (17.0%) than in fish and vegetarian dishes. Among these, the vegetables were the most wasted (25.3% and 27.9%, respectively). Conclusion: This work presents some insights to future interventions in the direction of a healthier and more sustainable foodservice.