Proper fertilizer management and applications could effectively reduce global warming potential (GWP) by reducing GHG emissions and improve soil fertility under cereal production. However, the effect of soil fertilizer management practices on GWP and soil fertility is less understood in the agricultural soils of Ethiopia. The present study evaluated the effects of fertilizer application strategy on GWP, and soil fertility in a Nitisol. Both field and laboratory incubation experiments were conducted with the same treatments in Ethiopia and at the University of Rostock, Germany, respectively. Seven treatments (Cont: no input; 100min: 100% mineral fertilizer, 80min: 80% mineral fertilizer + 1.4 t ha^–1 compost; 60min: 60% mineral fertilizer + 2.8 t ha^–1 compost; 50min: 50% mineral fertilizer + 3.5 t ha^–1 compost; 30min: 30% mineral fertilizer + 4.9 t ha^–1 compost, and 100comp: 100% compost) with four replications were applied on maize crop (Zea mays L. Bako hybrid 661) for two-consecutive growing seasons. The laboratory incubation experiment was also performed with two moisture levels (40% and 75% of water-filled pore space) to simulate the seasonal rainfall pattern. GWP was calculated by summing up the quantified gas emissions of nitrous oxide (N₂O), carbon dioxide (CO₂), and methane (CH₄). The laboratory result for GWP showed that soil fertilized with mineral fertilizer alone was significantly (p < 0.05) increased by 27.1%–34% of the average GWP value compared to combined fertilizer treatments in the soil at a moisture level of 75%. From the field experiment, most plant nutrients were significantly improved in combined fertilizer treatments compared to sole mineral fertilizer application. For example, carbon, calcium, magnesium, and potassium were increased by 26.21–39.81%, 73.2–168.8%, 146.6–251.5%, and 47–99% respectively in combined fertilizer in comparison to 100min treatment. The study revealed that combining 30 or 50 kg N ha^‒1 of mineral fertilizer with biowaste compost (4.9 or 3.5 t ha^–1) would be a suitable combination to mitigate the GWP and improve soil quality in smallholder farming systems, due to a slow release of N during decomposition into the soil compared to mineral fertilizer alone. However, to evaluate GWP under the field conditions, future investigations would be recommended.