Estimates of cropland nutrient budgets and nutrient use efficiencies at national to global scales generally rely on average nutrient concentrations for quantifying nutrients removed in crop yield and by-products. Given the relevance of crop removal in nutrient budgets, it is important that more locally relevant coefficients or models are developed. However, many countries do not have sufficient data from farm surveys or field experiments. Using maize as an example, we assessed how much a country’s estimated nutrient removal is affected when using either global (Tier 1), regional (Tier 2) or national/sub-national (Tier 3) estimates of harvest index and nutrient concentration of crop products and residues. Estimates of cropland removal of nitrogen, phosphorus and potassium varied substantially (up to 52%), depending on which Tier approach was used. This had a substantial influence on national nutrient budgets and nutrient use efficiencies. Our study shows the large uncertainty associated with current nutrient offtake estimates. If national data (Tier 2) are not available, Tier 3 offers a methodology to overcome such data limitations through the application of models, trained on localized but widely available data for countries. We recommend to use Tier 2 or Tier 3 approaches once they have been evaluated against real on-farm data. The presented methodology can be applied to other crops and nutrients to improve cropland nutrient budgets and estimates of crop nutrient use efficiencies.