In sub-Saharan Africa, agriculture can account for up to 66% of anthropogenic greenhouse gas (GHG) emissions. Unfortunately, due to the low number of studies in the region there is still much uncertainty on how management activities can affect these emissions. To help reduce this uncertainty, we measured GHG emissions from three maize (Zea mays) growing seasons in central Kenya. Treatments included: (1) a no N application control (C); (2) split (30% at planting and 70% 1 month after planting) mineral nitrogen (N) applications (Min—100 kg N ha⁻¹); (3) split mineral N + irrigation (equivalent to 10 mm precipitation every three days—MI); (4) split mineral N + 40 kg N ha⁻¹ added as manure (MM—total N = 140 kg ha⁻¹); and (5) split mineral + intercropping with faba beans (Phaseolus vulgaris—MB). Soil CO₂ fluxes were lower in season 1 compared to seasons 2 and 3 with fluxes highest in Min (p = 0.02) in season 2 and lowest in C (p = 0.02) in season 3. There was uptake of CH₄ in these soils that decreased from season 1 to 3 as the mean soil moisture content increased. Cumulative N₂O fluxes ranged from 0.25 to 2.45 kg N₂O-N ha⁻¹, with the highest fluxes from MI during season 3 (p = 0.01) and the lowest from C during season 1 (p = 0.03). The average fertilizer induced emission factor (0.36 ± 0.03%) was roughly one-third the default value of 1%. Soil moisture was a critical factor controlling GHG emissions in these central Kenya highlands. Under low soil moisture, the soils were CH₄ sinks and minimal N₂O sources.