Sub Saharan Africa (SSA) is faced with increasing food demand to meet population pressures and combat high variability of seasonal rainfall.  Agricultural intensification to overcome these problems is relying on heavy tillage disturbance and high fertilizer inputs.  Consequently, current agricultural practices have brought declining environmental services, such as increased soil erosion, soil fertility degradation and increased greenhouse gas emissions (GHG).  While CAPS have been successfully implemented in temperate regions of the world, only limited success of the adaptation has been reported in tropics, especially in Sub-Saharan Africa. This research is a part of a larger project that deals with the development and transfer of conservation agricultural production systems in Western Kenya and Eastern Uganda funded by SANREM CRSP. The objective of this research is to assess the effects of maize (Zea mays) intercropped with common bean (Phaseolus vulgaris) and alternative cropping practices that include maize together with a legume cover crop, velvet bean (Mucuna pruriens) as intercrop, relay crop or strip intercrop, on GHG emissions  under low input practices. We hypothesized that the use of cover crop in conjunction with reduced tillage will result in lowering GHG emissions and improvement of crop yield and soil carbon (C) and nitrogen (N).  This paper will discuss the preliminary results from the first long rainy season of March- August 2011.