Fertility management techniques being promoted in sub-Saharan Africa (SSA) seek to grow indigenous vegetables economically and sustainably. This study was conducted in a phytotron chamber and compared yield, soil carbon (C) speciation and greenhouse gas (nitrous oxide (N₂O) and carbon dioxide (CO₂)) emissions from SSA soils of two ecoregions; the dry savanna (lna, Republic of Benin) and rainforest (Ife, Nigeria) cultivated with local amaranth (Amaranthus cruentus) under manure (5 t/ha) and/or urea (80 kg N/ha) fertilization. Vegetable yield ranged from 1753 kg/ac to 3198kg/ac in the rainforest, RF, soils and 1281 kg/ac to 1951 kg/ac in the dry savanna, DS, soils. Yield in the urea treatment was slightly higher compared to the manure+urea treatment, but the difference was not statistically significant. Cumulative CO₂ emissions over 21 days ranged from 497.06 to 579.47 g CO₂ in the RF, and 322.96 to 624.97 g CO₂ in the DS, while cumulative N₂O emissions ranged from 60.53 to 220.86 mg N₂O in the RF, and 24.78 to 99.08 mg N₂O in the DS. In the RF samples, the combined use of manure and urea reduced CO₂ and N₂O emissions but led to an increase in the DS samples. ATR-FTIR analysis showed that the combined use of manure and urea increased the rate of microbial degradation in the soils of the DS, but no such effect was observed in soils of the RF. We conclude that combining manure and urea fertilization has different effects on soils of the two ecoregions, and that RF farmers can reduce agricultural emissions without compromising soil productivity and yield potential.