Processed food products present high energy intensity, along with a large amount of food losses and waste. The recovery of residual biomass as integrated renewable energy source could represent an interesting option for the substitution of fossil energy, contributing to the transition of agro-food sector towards a low-carbon economy. Two scenarios were compared, in order to evaluate the impacts of a fossil fuel-based food chain and the potential benefits of the integration of bioenergy production, using peach nectar as case study. In the first scenario, peach nectar is produced, distributed and consumed using fossil energy, while residuals are wasted. In the second scenario, byproducts from the nectar chain are used to produce bioenergy from combustion or anaerobic digestion, which is then consumed to substitute electricity and heat. A comparative life cycle assessment (LCA) based on the same functional unit was performed. Main results show that, in the conventional scenario, most of the damage derives from land use, especially for sugar and glucose production, from the fossil energy consumption of about 15 MJ l−1, and the related greenhouse gas (GHG) emissions of 0.91 kg CO2 eq l−1. Food waste leads to a loss of about 20 kcal l−1. Bioenergy integration would allow a 13–15% damage reduction, mainly due to the substitution of indirect energy consumption. The effects on human health and ecosystem quality are limited.