Soil nutrient budget is one of the critical concerns in most farming systems, especially in degraded environments. This paper reveals a net nutrient removal from the agricultural system that resulted in negative budgets, particularly for N. Large variations existed between villages, with N budget ranging from -9.6 to -252.4 kg/ha/year, with a mean budget of -91.9 kg/ha/year. Various factors seem to have contributed to the negative budgets, including soil erosion, crop harvest and residue removals. The latter two contributed significantly less to nutrient losses compared to soil erosion. The main input sources for nutrients into the system were found to be manure, crop residues, atmospheric deposition and to a limited extent inorganic fertilisers. Manure application added into the soil about 13, 1.5, and 0.04 kg/ha/year of N, P and K respectively. Its use was, however, limited by the inadequate amounts available. Crop residues added about 3.9, 1.9 and 11 kg/ha/year of N, P and K respectively. The use of crop residues for nutrient recycling and soil maintenance is however, constrained by its competitive use for animal feed. Generally, this farming system seems to be characterised by negative nutrient budgets, limiting agricultural productivity and sustainability.