Crop yield simulation using the Denitrification-Decomposition (DNDC) model can help to understand key bottlenecks for improved nitrogen (N) use efficiency and estimate greenhouse gas (GHG) emissions in West African urban vegetable production. The DNDC model was successfully calibrated using high-resolution weather records, information on management practices and soils, and measured biomass accumulation and N uptake by amaranth (Amaranthus L.), jute mallow (Corchorus olitorius L.), lettuce (Lactuca sativa L.), and roselle (Hibiscus sabdariffa L.) for different input intensities (May 2014-November 2015) in urban vegetable production of Tamale (N-Ghana, West Africa). The root mean square error (RMSE) and relative error (E) values fell within the confidence interval (α 5%) of the measurements, and there was a high correlation (0.91 to 0.98) between measurements and predictions. However, the analysis of uncertainty and factor importance indicated that soil properties (pH, SOC, and clay content) and weather (precipitation) variability contributed highly to yield uncertainty of vegetable biomass.