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Smallholder farmers in western Kenya who plant maize (Zea mays L.) intercropped with beans (Phaseolus vulgaris L.) face many challenges associated with nutrient-poor soils and weather-related crop failures. In regions where temperatures are favorable, crops are grown twice per year during long and short rainy seasons and in other regions, once per year during one long growing season. Growing crops two times per year necessitates frequent land preparation using inversion-type tillage. Little is known about the impact of current tillage-intensive crop management on annual soil organic matter (SOM) recovery. The aim of this study was to assess changes to soil carbon (C), nitrogen (N) and crop performance in typical maize-bean production during long rainy season (LR), short rainy season (SR) and a fallow period (FP) in areas where crops are grown one time (Trans-Nzoia) and two times per year (Bungoma). The two locations were sampled three times per year for a period of three years. Soils were analyzed for potentially mineralizable nitrogen (PMN), ammonium (NH4), nitrate (NO3), water filled pore space (WFPS), nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2). Results demonstrated significantly greater PMN, NH4 N2O and CO2 during SR in Bungoma compared with LR and FP suggesting high C and N mineralization caused by warmer temperatures and high frequency of tillage. Soils in Trans-Nzoia also showed elevated NH4, NO3 and N2O during the same period but the magnitude of these changes was much lower compared with Bungoma. Mineralization negatively impacted annual SOM renewal and crop production as further demonstrated by low soil total C and N and cumulative crop yields in Bungoma. Planting edible cover crops, reducing tillage and using manure should become a necessity to support sustainable crop production. Particular attention should concentrate on designing appropriate management strategies for SR season in Bungoma.