We quantified the soil carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes of five soil fertility management practices (inorganic fertilizer (Mf), maize residue + inorganic fertilizer (RMf), maize residue + inorganic fertilizer + goat manure (RMfM), maize residue + tithonia diversifolia + goat manure (RTiM), and a control (CtC)) in Kenya’s central highlands using a static chamber method from March 2019 to March 2020. The cumulative annual soil CH4 uptake ranged from −1.07 to −0.64 kg CH4-C ha−1 yr−1, CO2 emissions from 4.59 to 9.01 Mg CO2-C ha−1 yr−1, and N2O fluxes from 104 to 279 g N2O-N ha−1 yr−1. The RTiM produced the highest CO2 emissions (9.01 Mg CO2-C ha−1 yr−1), carbon sequestration (3.99 Mg CO2-eq ha−1), yield-scaled N2O emissions (YSE) (0.043 g N2O-N kg−1 grain yield), the lowest net global warming potential (net GWP) (−14.7 Mg CO2-eq ha−1) and greenhouse gas intensities (GHGI) (−2.81 Kg CO2-eq kg−1 grain yield). We observed average maize grain yields of 7.98 Mg ha−1 yr−1 under RMfM treatment. Integrating inorganic fertilizer and maize residue retention resulted in low emissions, increased soil organic carbon sequestration, and high maize yields.