The agri-food sector accounts for 26% of the EU energy consumption, where 28% of this energy belongs to natural resource processing. As multiple products are produced on the same line and numerous process steps are interrelated, the energy use in this industry is complex in general. Moreover, bottom-up data analysis of how much energy processes are used, and furthermore, why and where opportunities for improvements exist, are less prevalent. This paper proposes a methodology for estimating the energy consumption of the agri-food processing. The collection of real data from several industrial enterprises in Germany as part of research programs enabled an accurate assessment of energy consumption and savings.