AbstractFood, feed, and fiber production needs to increase to support demands of the growing population in Sub‐Saharan Africa (SSA), while soil fertility continues to decline. Intercropping, the cultivation of two or more crop species on the same field, can provide yield benefits and is suggested to positively affect soil organic carbon (C) and nitrogen (N) stocks. This study uses the biogeochemical model system LandscapeDNDC with the objective to (a) represent maize‐legume intercropping systems in different bioregions in SSA by simultaneously simulating both crops and their interactions and (b) assess long‐term (20 years) impacts of intercropping under varying mineral fertilizer inputs (0–150 kg N ha−1 yr−1) on productivity as well as soil organic C and N stocks. We test LandscapeDNDC on 82 field data sets (site‐year‐treatment combinations) from 18 sites to represent yields and soil C/N dynamics of maize‐legume intercropping systems. Using the model for long‐term scenario simulations showed that intercropping allows to sustain productivity and to improve or maintain SOC stock in low or zero fertilizer systems if all residues are returned to the soil. In contrast, for sole‐cropped maize systems, a decline in SOC stocks was simulated unless a minimum of 35 kg N ha−1 yr−1 of fertilizer was applied at full residue return. We conclude that intercropping using legumes alongside sufficient residue return allows for stabilizing long‐term yields while avoiding SOC losses even with low fertilizer N inputs. Overall, our study confirms the potential of intercropping as a sustainable agricultural practice that could significantly contribute to food security in SSA.