The contribution of smallholder farming systems to the National greenhouse gas (GHG) budget is missing in most developing countries, including Kenya. Data on the contribution of smallholder cropping systems to the GHG balance is essential for realising Sustainable Development Goal 13 on climate action, i.e., on nationally determined contributions (NDCs) and in compliance with the Paris Agreement. Do smallholder farming systems act as nature-based solutions for greenhouse gas emissions reduction? This study evaluated GHG emissions from cropping systems under on-farm smallholder farming conditions. We had five cropping systems on two smallholder farms: sole maize, maize-bean intercrop, coffee, banana, and agroforestry. Gas samples were collected using three static chambers per cropping system. The gas samples were analysed using gas chromatography (GC) fitted with a 63Ni-electron capture detector (ECD) for N2O and flame ionisation detector (FID) for CH4 and CO2 using N as carrier gas. Cumulative annual fluxes of (CH4, N2O, and CO2) varied significantly in farms one and two across the cropping systems. The cumulative soil GHG fluxes ranged from -1.34 kg CH4-C ha−1 yr−1 under agroforestry to -0.77 kg CH4-C ha−1 yr−1 under banana for CH4, 0.30 kg N2O-N ha−1 yr−1 to 1.23 kg N2O-N ha−1 yr−1 for N2O and 5949 kg CO2-C ha−1 yr−1 to 12954 kg CO2-C ha−1 yr−1 for CO2. The maize grain yields ranged from 0 to 3.38 Mg ha−1. The N2O yields scaled emissions ranged from 0.10 to 0.26 g kg−1 maize and 0.68 to 1.30 g kg−1 beans. Smallholder farmers in Upper Eastern Kenya contribute a limited amount of soil GHG emissions and thus could act as a nature-based solution for lowering agricultural emissions.