The environmental impacts of food systems and the health consequences of excess food intake are well-acknowledged global issues. However, the climate impact of excess food intake, or metabolic food waste, has received less attention. This study estimated the amount of metabolic food waste and its climate impact in Sweden. Excess food intake was estimated based on the adult overweight and obesity prevalence in Sweden, by applying two alternative calculation methods, one based on the energy content of excess body fat, and the other based on the excess energy intake due to excess body fat. These caloric values were translated to food consumption patterns according to three dietary scenarios and their climate impact estimated based on carbon footprint data. The results showed that the annual amount of metabolic food waste represented 480–710 kt of food in Sweden and, regardless of dietary scenario, exceeded the annual amount of avoidable household food waste. The estimated greenhouse gas emissions from the metabolic food waste amounted up to 1.2 Mt CO2e annually, accounting for approximately 2% of the total and 10% of the food-related climate impact in Sweden. This study confirms the magnitude of the hidden climate cost of excess food intake on a national level and emphasizes the importance of taking this aspect into consideration in actions to improve both planetary and human health. Although applied to the Swedish context, the methodology used in the present study could also be used to assess the environmental impact of excess food intake in other countries globally.