This paper develops an innovative approach for calculating household nutrition indicators in a Computable General Equilibrium framework, using the flow of primary agri-food commodities through the global economy from farm to fork. It has been incorporated as a nutrition module in MAGNET. The method of tracing nutrients through the food system allows for making agriculture, the food supply chain and the economy as a whole nutrition-sensitive in scenario analyses. The validation of the nutrition outcomes in the base year with global data on nutrient consumption from the FAO reveals important differences which stem from differences in data and assumptions. Various solutions are identified to improve the calculations in the future. In the short run, correction factors are applied in the calculation of indicators in the nutrition module to capture and adjust the methodology for the remaining differences.