It is challenging to quantify the production of wood-based biomass, to define the type and where it comes from, how it is used, and the amount that remains available. This information is crucial for the implementation of national and transnational regulations and is a pillar for the development of the future bio-based circular economy. A variety of studies estimate the production of biomass, performs material flow analyses, or addresses supply chain modelling. These studies are often built upon distinct assumptions, tailored to a specific purpose, and often poorly described. This makes comparison amongst studies, generalization of results, or replication hard to even impossible. This paper presents a comprehensive methodology for wood-based biomass material flow analysis, anchored in Material Flow Analysis, built upon literature review and deducted through systematization of previous studies. This is a five-step approach, consisting of (1) adopt proper terminology; (2) obtain accurate estimates for the biomass flows; (3) Sankey diagram for resource balance representation; (4) scenario analysis; (5) stakeholders validation. The focus is to provide instructions for producing a generalized Sankey diagram, from the categorization of biomass resources, uses/applications in a circular economy setting, towards the development of scenario analysis. Its practical implementation is presented by defining the yearly wood-based biomass resource balance of Portugal and the waste wood resource balance of Flanders. The main data sources for the quantification of the biomass sources and uses/applications are identified. Based on the insights from these case studies, our methodological approach already shows to be replicable and with comparable results. This enables the comparison of resource flows between different regions and countries and also monitoring the progress over time. This leads to improved data which can be instruments for supporting companies’ decision-making processes (e.g., infrastructure investments or other strategic decisions), as well as designing policy strategies and incentives.