To decarbonize the European Union, protein consumption must transition to diets low in meat and dairy which will drastically change the material and energy flows in current meat and dairy supply chains. To understand the impacts on current flows, a baseline is required. Although recent studies have improved the scope of reported greenhouse gas (GHG) emissions, no quantitative overview exists including intermediate and final product flows. To address this knowledge gap, we structured the meat and dairy supply chains into a connected set of transformation nodes and distribution nodes. The former are processes transforming inputs into outputs, whereas the latter distribute the outputs to other processes using them as inputs. Currently, livestock play a central role in agriculture and other industries through the consumption of 271 Mt fodder crops, 108 Mt grain, 85 Mt grazed biomass, 49 Mt oil meal, and 16 Mt feed by-products. This feed is transformed into 64 Mt dairy and 35 Mt meat which ensures that the EU28 is a net exporter of meat and dairy while providing 25 Mt of by-products. This production also leads to 435 Mt CO2-eq. with the main contribution from beef cattle (35%), dairy cattle (32%), and swine (20%). Thus, the lower GHG intensities of dairy products compared to meat do not imply a low contribution to the total emissions. By mapping the material, energy, and GHG emission flows, we have created a baseline suitable for identifying potential supply chain changes and their related GHG increase or decrease resulting from the protein transition.@en