Special problems arise when analyzing supply chains because of the complexity of the relationships in the system. In addressing this concern for a research project on a vegetable supply chain in Mindanao,the authors of this paper use a pluralistic methodology. A soft-systems framework was used to structure and analyze the problem and identify relevant systems. Issues addressed are the extent of efficiency along the supply chain (including input supply (issues), output marketing, quality control and transport) and the relationships between the various participants in the supply chain. Qualitative and quantitative data collection methods have been used.