Special problems are presented when analysing supply chains because of the complexity of the relationships. In addressing this problem for a vegetable supply chain in Mindanao a pluralistic methodology is used. A soft systems framework was used to structure and analyse the problem and identify relevant systems. Issues we are addressing are efficiencies along the supply chain (including input supply issues, output marketing, quality control and transport) and relationships between the various participants in the supply chain. Qualitative and quantitative data collection methods have been used. Analysis is being conducted with qualitative data analysis techniques, LP farm household models, transaction cost economics, gap analysis, factor analysis and structural equation modelling.