A soil nutrient balance is a commonly used indicator to assess changes in soil fertility. In this paper, an earlier developed methodology by Stoorvogel and Smaling to assess the soil nutrient balance is given a major overhaul, based on growing insights and advances in data availability and modelling. The soil nutrient balance is treated as the net balance of five inflows (mineral fertilizer, organic inputs, atmospheric deposition, nitrogen fixation and sedimentation) and five outflows (crop products, crop residues, leaching, gaseous losses and erosion). This study aims to improve the existing methodology by making it spatially explicit, improving various transfer functions, and by modelling explicitly the uncertainties in the estimations. Spatially explicit modelling has become possible through a novel methodology to create a simulated land use map on the basis of the principles of traditional qualitative land evaluation. New literature data on the various inputs and outputs allowed improvement of the estimations of deposition, sedimentation, leaching, and erosion. Moreover, the uncertainty of the calculated soil nutrient balances was assessed. To illustrate the improved methodology, we applied it to Burkina Faso and revealed that nutrient depletion is occurring throughout the country at rates of Ă20 AE 15 kg N ha Ă1 , Ă3:7 AE 2:9 kg P ha Ă1 and Ă15 AE 12 kg K ha Ă1 . The resulting spatial soil nutrient balances at the national level can constitute the basis for targeting soil fertility policies at lower levels.