This paper outlines methodological frameworks for conducting research and development with agribusiness supply chains in transitional economies where the objective is to improve the competitiveness of the supply chains in a global environment. The key difficulty when operating with supply chains is the complexity of the issues involved because constraints can occur from production by small farmers through to the relationship between retailers and consumers. Failure to address key constraints can lead to failure to have any impact. This creates problems for integrating research, because researchers are generally trained in disciplines that cover only a small proportion of the issues and operate from differing epistemologies. The other difficulty is to incorporate a framework for change management, since good research is not much use unless it leads to positive outcomes. A framework for managing these problems is outlined, which has been developed and trialled in work with vegetable supply chains in the Philippines and coffee supply chains in PNG. The framework incorporates a dualistic agribusiness systems model for mapping the chain issues and combines this with a pluralistic framework derived from Checkland’s soft systems methodology for research analysing the system. This is integrated with a participatory action research methodology for change management.