Abstract Soil nutrient loss due to soil erosion and removal in harvest with traditional farming methods where farmers do not use any fertilisers threatens the sustainability of vegetable productions in the Philippine uplands. Consequently, poor farmers are losing incomes due to declining yields. The situation is reaching crisis point. A bio-economic analysis is used in this research to investigate the economic returns in terms of gross and net annual income over time for upland farmers from adopting alternative soil management options. Cost benefit analysis is used to compare the net returns to farmers from potential management options. A bio-physical model, SCUAF, is used to simulate the long-run tomato yields and associated soil erosion, over a seven-year period, for different soil management options which are both income enhancing and soil nutrient preserving. Data obtained through experiments and surveys of upland farmers in Claveria in the Philippines island of Mindanao, are used to derive yearly production budget for tomato farming on one hectare of land. The analyses reveal that significantly higher economic returns are achievable a combination of organic and inorganic fertiliser additions. This combination seems to be most attractive since it leads to benefits in both yield increase and reduced soil erosion over time. Therefore, concentrating further research on the use of fertiliser combinations, especially at lower rates where marginal returns are highest seems to be an appropriate focus, and one which is most likely to be adopted by farmers.