Abstract The paper provides a framework that focuses on the linkages between several key dimensions of supply chain organization and performance of perishable tropical food products. The focus is on the relationship between governance regime and quality management. However, two other but related variables are taken into account because they impact on the relationship between governance and quality management. These variables are channel choice and value added distribution in the supply chain. Governance regime is reflecting how to enhance coordination and trust amongst supply chain partners and how to reduce transaction costs. Quality management is dealing with how to manage food technology processes such that required quality levels can be improved and variability in quality of natural products can be exploited. Governance regimes in relation to quality management practices are discussed to the extent that supply chain partners are able, or are enabled, to invest in required quality improve-ments. Reduction of transaction costs, creation of trust-based networks and proper trade-offs between direct and future gains may offer substantial contributions to effective quality management and enforcement. This framework has been applied to nine case studies on smallholder-based food supply chains originating from developing countries (Ruben et al., 2007). Three of these case studies are discussed in this paper to illustrate what challenges can be derived from the case studies. The selected case studies concern fish originating from Kenya, mango originating from Costa Rica and vegetables produced in China.