Low nitrogen use efficiency and fertilizer recovery by crops in sub-Saharan Africa suggests high rates of nitrogen and carbon leaching, resulting in greenhouse gas emissions. The objective of this study was to inventory seasonal GHG emissions from continuous maize/bean intercropping grown under unimodal (one growing season) and bi-modal (two growing seasons) conditions. Soils from the bimodal area of Bungoma had very high N2O emissions during crop growth and greater though still very low CH4 assimilation compared to Trans-Nzoia.