This paper provides a multi-stage multi-layer mapping methodology for capturing the macro-level supply chain dynamics that govern industrial systems using renewable feedstocks. The mapping approach combines the Industrial Systems Mapping and System Dynamics principles to systematically capture the interrelations across: (i) institutional players, (ii) sector specialists, (iii) products and intermediates, (iv) production operations, and (v) firms within the supply chain. The interfaces are further explored at four interconnected and mutually interacting theme areas of analysis, namely: (i) renewable chemical feedstocks, (ii) production technologies, (iii) target markets, and (iv) value and economic viability. We demonstrate the applicability of our approach by mapping the dynamics in industrial systems for the production of ‘green’ pharmaceuticals, particularly via the illustrative case of paracetamol. Through the use of the proposed integrated mapping process the case study demonstrates the principal interrelationships and inter-firm dynamics between the different layers of analysis. Three main drivers are identified that could enhance supply network transformations for improved viability of these developing industrial systems, namely: (i) regulatory conformance with market requirements, (ii) system level feasibility assessment of given renewable feedstocks, and (iii) target market volume demand. The causal feedback elements of the provided mapping technique indicate that it could support the analysis of industrial systems’ transformation dynamics enabled by renewable feedstocks. The standardisation of the methodology and its elements provides for an effective visualisation technique with cross-industry relevance.