Crop production is the single largest cause of human alteration of the global nitrogen cycle. We present a comprehensive assessment of global nitrogen flows in cropland for the year 2000 with a spatial resolution of 5 arc-minutes. We calculated a total nitrogen input (IN) of 136.60 trillion grams (Tg) of N per year, of which almost half is contributed by mineral nitrogen fertilizers, and a total nitrogen output (OUT) of 148.14 Tg of N per year, of which 55% is uptake by harvested crops and crop residues. We present high-resolution maps quantifying the spatial distribution of nitrogen IN and OUT flows, soil nitrogen balance, and surface nitrogen balance. The high-resolution data are aggregated at the national level on a per capita basis to assess nitrogen stress levels. The results show that almost 80% of African countries are confronted with nitrogen scarcity or nitrogen stress problems, which, along with poverty, cause food insecurity and malnutrition. The assessment also shows a global average nitrogen recovery rate of 59%, indicating that nearly two-fifths of nitrogen inputs are lost in ecosystems. More effective management of nitrogen is essential to reduce the deleterious environmental consequences.