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 -1.34kg CH₄C ha⁻¹ yr⁻¹ under agroforestry to -0.77kg CH₄C ha⁻¹ yr⁻¹ under banana for CH₄, 0.30kg N₂ON ha⁻¹ yr⁻¹ to 1.23kg N₂ON ha⁻¹ yr⁻¹ for N₂O and 5949kg CO₂C ha⁻¹ yr⁻¹ to 12,954kg CO₂C 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 0.26g kg⁻¹ maize and 0.68 to 1.30g 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.