Increasingly, food security interventions in developing economies are adapting value chain approaches to facilitate the integration of smallholders into high margin value chains. In Kenya, the resurgence of African Indigenous Vegetables due to their medicinal value and rich micronutrients is a case in point. The vegetables are cultivated by smallholders, and the supply has not matched the demand in the high margin markets among urban consumers. Access to such high margin markets necessitates that smallholders gain entry or upgrade into the networks of those buyers who possess considerable control of these value chains. There is limited value chain scholarship on chain governance and its implication for smallholder participation in Kenya. This study investigated how value chain governance influences farmer participation in vegetable markets and food security in Kenya. This study employed exploratory case study design to provide chain architecture, isolate primary actors, their roles, relations, constraints and opportunities for upgrading by smallholders. A mixed method approach involving a multistage sampling technique of 339 respondents was employed to bring to the surface insights on chain architecture, market margins and governance structures and their implications as regards upgrading trajectories for small-scale farmers in Kenya. Thematic analysis was used for data analysis. Spot market relations were found to dominate traditional value chains in rural areas while peri-urban areas exhibited both traditional and coordinated value chains. The value chains are characterized by very weak linkages between upstream actors and downstream partners, where wholesalers and supermarkets play the role of leading firms in traditional and coordinated value chains, respectively. The study recommends the inclusion of famers in market management committees and the establishment of binding contractual arrangements with supermarkets.