This case study examined performance of rural cassava SMEs managed by small scale farmers in Busia and Kisumu Counties in the lake region of Kenya. Formal survey, focus group discussions and key informant interviews were used to collect data from farmers and stakeholders in the region. The data were analysed descriptively using proportions (percentages and proportions), means and standard deviation and inferentially, using statistical tests of significance. The findings revealed gross inefficiencies in the management of cassava SMEs. Grass-root SMEs lack professional managers and exhibit inadequate organizational, quantity and quality management, high operational costs, lack of trust from farmers, inadequate financing, weak technical, agribusiness skills and weak linkages with markets. The findings challenge promotion of farmer-led organizations in rural areas to perform additional roles such as processing and marketing functions beyond their core business which is production. To remain relevant in a competitive value chain, grass-root farmer-led SMEs need to be re structured into viable economic entities with clear market-orientation. Ordinary smallholder farmers should specialize in producing sufficient quantity and quality of agricultural commodities, while processing and marketing functions are taken up by professional entrepreneurs. This study recommends an entrepreneur model rather than farmer-led SMEs as potentially best suited in creating efficiency in the cassava value chain in the lake region of Kenya.