The aim of the study was to explore the currently unexploited potential of agrifood waste and by-product biomasses for energy recovery and nutrient recycling, to mitigate climate change and eutrophication. The technical potential was assessed in two different case regions in Finland using two contrasting processing technologies, one oriented to recycle carbon and the other one to maximise replacement of fossil energy. The reduction in nutrient surplus through efficient recycling of biomass and consequent decline in fertiliser use was calculated. The reduction in GHG emissions was estimated based on the replacement of fossil energy and the diminished fertiliser manufacture. It was established that the full potential of use of the biomass to reduce GHG emissions can only be exploited in biorefineries that both produce energy and efficiently recycle nutrients. Such biorefineries have the potential to significantly mitigate climate change and prevent eutrophication. The potential reduction in GHG emissions corresponded to a third of agricultural emissions, and the reduction in fertiliser manufacture contributed with an additional fifth of that. The energy recovery corresponded to 5–10% of the fossil energy used in the regions, and the reduction in energy use for manufacture of fertilisers represented an additional 14–20% in comparison with that. The potential for nutrient recycling corresponded to 99–120% of P and 45–72% of N in the yields harvested in the regions. The choice of technology had a more pronounced impact on energy recovery, GHG emissions and C budget than on nutrient recycling.