Several attempts have been made to harmonize guidelines for environmental footprints of food and beverages. For example, the food Sustainable Consumption and Production Roundtable, the Leap partnership, and the Environmental Footprint project, in particular within the Cattle Model Working Group. Despite all these activities, there are still many issues unresolved. This paper gives an overview of five important reasons why it is so difficult to reach consensus within the sector. In short, the issues are: 1) how to allocate deforestation to land use activities; 2) how to assess agricultural emissions profiles; 3) how to make regionalized water scarcity assessments; 4) how to choose the functional unit of food and beverages; and 5) how to deal with multi-functional processes in agro-industry. Recommendations as motivated in this paper are, in summary, to: 1) use the method to calculate the amount of land use change caused by increased pressure from growing areas per crop in each country; 2) always calculate agricultural emissions using at least an intermediate level of detail with the option to add more detail; 3) use good quality irrigation and crop evapotranspiration data, and at least country specific water scarcity factors; 4) report the environmental footprint results per unit of economic value besides per unit of mass or volume to enable fairer comparisons; 5) and apply economic allocation in all multi-functional agricultural and agri-industrial processes based on realistic prices calculated as multiple year averages.