We conducted an ex ante evaluation of soil fertility management strategies on soil organic matter (SOM), nitrogen balance, greenhouse gas (GHG) emissions, and profitability under three important scenarios: (1) inorganic fertilizers, (2) organic manure, and (3) combined organic manure and inorganic fertilizers. Focus group discussions and household surveys were used to collect data in Rakai, Uganda, and Lushoto, Tanzania. We assessed impact for three farm types (small scale, medium scale, and large scale) using a bioeconomic model: FarmDESIGN. Our main findings are as follows. First, whereas in Lushoto the combined use of organic manure and inorganic fertilizers contributed the most to SOM relative to the baseline for all farm types, in Rakai the same scenario had greater impacts for only medium- and large-scale farms. For small-scale farms, improvement in SOM mostly came from the use of inorganic fertilizers. Second, in both countries, nitrogen balance increased across all scenarios and farm types. Third, the increase in SOM and nitrogen balance was accompanied by an increase in GHG emissions, especially for scenarios with manure or combining manure and inorganic fertilizers. Fourth, impacts were mixed in terms of profitability. In Lushoto, Tanzania, the smallscale farm has the lowest operating profit, while the large-scale farm has the highest. In Rakai, Uganda, gross margins from crops contributed the largest share to farm profitability. Our findings not only suggest increased soil fertility with the adoption of improved management strategies but also highlight potential trade-offs in terms of increased emissions and reduced profitability for some farm types. Taking into account both synergies and trade-offs when promoting soil fertility management strategies might yield successful efforts.