In recent years, improvements in the global food system have greatly enhanced nutritional status worldwide. However, the rise in unhealthy diets has contributed to higher risks of lifestyle-related diseases, and large-scale food production has been reported to significantly affect multiple environmental domains. In this study, we conducted an integrated assessment of 9,429 recipes listed on a Japanese website by converting both environmental impacts, from ingredient production through cooking and disposal, and the health effects of food and nutrient intake into Disability-Adjusted Life Years (DALYs). For environmental health impacts, we targeted five domains—climate change, ozone depletion, air pollution, photochemical oxidants, and water consumption—and employed Japan’s inventory database IDEA v3.4.1, along with the LIME3 impact assessment method, to calculate DALYs. Regarding the health effects of food and nutrient intake, we referred to dietary risk factors reported in the Global Burden of Disease (GBD) and identified 11 items associated with disease risks due to overconsumption or insufficient intake. Their effects on health were evaluated in DALYs using GLAM coefficients. Analysis of 3,772 recipes classified as main dishes revealed that beef-based recipes produced the largest environmental health impact, while chicken- or seafood-based dishes exhibited low variability and suggested potential health benefits. Specifically, the 25th percentile of beef dishes exceeded the maximum values for other groups, whereas chicken-based recipes had the smallest range, and many chicken or seafood dishes yielded integrated DALYs below zero, indicating health benefits. Vegetable-based recipes varied widely depending on consumption patterns, and even red meat dishes such as pork or beef could mitigate adverse effects by incorporating nuts, seeds, and vegetables. Ultimately, the results imply that reducing salt and emphasizing chicken or seafood, alongside nuts and vegetables, represents a healthy and sustainable dietary choice. Hence, it is critical to balance the intake of various nutrients, moderate the consumption of red meat, and enhance the use of fiber-rich ingredients, which can collectively lower DALYs while ensuring sufficient protein. By adopting these dietary patterns, individuals can simultaneously lessen environmental burdens and bolster overall health, thereby advancing a transition to more sustainable eating habits. Future work will involve more comprehensive evaluations at the meal-plan level, including biodiversity impacts, to refine proposals aligned with Japanese food culture. These findings provide valuable evidence for examining dietary options from both health and environmental perspectives, thereby laying the foundation for promoting a shift toward more sustainable eating habits.