Agricultural management practices are frequently non conservative and can lead to substantial loss of soil organic carbon and soil fertility, but for many regions in Africa the knowledge is very limited. To study the effect of local agricultural practices on soil organic carbon content and to explore effective ways to increase soil carbon storage, field experiments were conducted on an upland rice soil (Lixisol) in northern Benin in West Africa. The treatments comprised two tillage systems (no-tillage, and manual tillage), two rice straw managements (no rice straw, and rice straw mulch at 3 Mg ha−1) and three nitrogen fertilizer levels (no nitrogen, 60 kg ha−1, 120 kg ha−1). Phosphorus and potassium fertilizers were applied to be non-limiting at 40 kg P2O5 ha−1 and 40 kg K2O ha−1 per cropping season. Heterotrophic respiration was higher in manual tillage than no-tillage, and higher in mulched than in non-mulched treatments. Under the current management practices (manual tillage, with no residue and no nitrogen fertilization) in upland rice fields in northern Benin, the carbon added as aboveground biomass and root biomass was not enough to compensate for the loss of carbon from organic matter decomposition, rendering the upland rice fields as net sources of atmospheric CO2. With no-tillage, 3 Mg ha−1 of rice straw mulch and 60 kg N ha−1, the soil carbon balance was approximately zero. With no other changes in management practices, an increase in nitrogen level from 60 kg N ha−1 to 120 kg N ha−1 resulted in a positive soil carbon balance. Considering the high cost of inorganic nitrogen fertilizer and the potential risk of soil and air pollution often associated with intensive fertilizer use, implementation of no-tillage combined with application of 3 Mg ha−1 of rice straw mulch and 60 kg N ha−1 could be recommended to the smallholder farmers to compensate for the loss of carbon from organic matter decomposition in upland rice fields in northern Benin.