The great challenge of reducing soil nutrient depletion and assuring agricultural system productivity in low-income countries caused by limited synthetic fertilizer use necessitates local and cost-effective nutrient sources. We estimated the changes of the nitrogen budget of agricultural systems in the East African Community from 1961 to 2018 to address the challenges of insufficient nitrogen inputs and serious soil nitrogen depletion in agricultural systems of the East African Community region. Results showed that total nitrogen input increased from 12.5 kg N ha -1 yr -1 in the 1960s to 21.8 kg N ha -1 yr -1 in the 2000s and 27 kg N ha -1 yr -1 in the 2010s. Total nitrogen crop uptake increased from 12.8 kg N ha -1 yr -1 in the 1960s to 18.2 kg N ha -1 yr -1 in the 2000s and 21.8 kg N ha -1 yr -1 in the 2010s. Soil nitrogen stock increased from -2.0 kg N ha -1 yr -1 in the 1960s to -0.5 kg N ha -1 yr -1 in the 2000s and 0.3 kg N ha -1 yr -1 in the 2010s. Our results allow us to substantiate for the first time that soil nitrogen depletion decreases with increasing input of nitrogen in agricultural systems of the East African Community region. This suggests that increases in nitrogen inputs through biological nitrogen fixation and animal manure are the critical nitrogen management practices to curb soil nitrogen depletion and sustain agricultural production systems in the East African Community region in order to meet food demand for a growing population.