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The intensive use of nitrogen (N) fertilizers in maize (Zea mays L.) cropping in sub-Saharan Africa (SSA) contributes significantly to nitrous oxide (N2O) emissions. Due to limited data on emissions and emission factors (EFs) in SSA, this study investigates GHG emissions and proposes EFs under different fertilization regimes in maize cropping in Burkina Faso (West Africa). A randomized complete block design was used with five treatments: (i) control: no fertilizer (CK), (ii) cattle manure (M), (iii) chemical fertilizer (NPK), (iv) a combination of chemical fertilizer and cattle manure (NPKM) at the national recommended rate, and (v) farmers’ practices, which involve chemical fertilizer combined with manure at the farmers’ rate (NPKM+). Cumulative N2O emissions varied significantly among treatments (p < 0.05), with the highest under NPKM (2.86 kg N2O-N ha−1) and the lowest under CK (1.93 ± 0.11 kg N2O-N ha−1). NPKM also showed the highest methane (CH4) uptake (−0.62 kg CH4-C ha−1; p < 0.001), while CK exhibited an increasing trend (0.74 kg CH4-C ha−1). The highest N2O EF was recorded for NPK (0.37 ± 0.05%), 63% lower than the Intergovernmental Panel on Climate Change default value. Although NPKM treatment resulted in the highest global warming potential and maize yield, it also achieved the lowest greenhouse gas intensity per unit of yield, highlighting a more efficient trade-off between productivity and climate impact with nitrogen fertilizer use. NPKM+ was the most effective in maintaining high maize productivity with lower yield-scaled N2O emissions and GHG intensity. These findings suggest that an integrated approach combining organic and inorganic fertilizers can mitigate soil GHG emissions. Further research is needed to refine climate-smart fertilizer combinations for sustainable maize production in SSA.