Implementation of the circular economy is one of the priorities of the European Union, and energy efficiency is one of its pillars. This article discusses an effective use of agri-food industry waste for the purposes of waste-to-energy in biogas plants. Its basic objective is the comparative assessment of the eco-efficiency of biogas production depending on the type of feedstock used, its transport and possibility to use generated heat. The environmental impact of the analysed installations was assessed with the application of the Life Cycle Assessment (LCA) methodology. Cost calculation was performed using the Levelized Cost of Electricity (LCOE) method. The LCA analysis indicated that a biogas plant with a lower level of waste heat use where substrates were delivered by wheeled transport has a negative impact on the environment. The structure of distributed energy production cost indicates a substantial share of feedstock supply costs in the total value of the LCOE ratio. Thus, the factor affecting the achievement of high eco-efficiency is the location of a biogas plant in the vicinity of an agri-food processing plant, from which the basic feedstock for biogas production is supplied with the transmission pipeline, whereas heat is transferred for the needs of production processes in a processing plant or farm.