The transition of the current economic system from non-renewable and fossil-based towards a more sustainable system using renewable resources is a dedicated objective of the German Na-tional Bioeconomy Strategy. In order to provide sound information on the status of the bioecon-omy, a monitoring concept that assesses the bio-based resources and sustainability effects associ-ated with German bioeconomy was developed. The general monitoring approach includes a definition of the bioeconomy and its implementation in terms of material flows and economic sectors at a given point in time. Based on this, available data is collected and bio-based material flows and economic sectors are quantified. These quanti-fications are used in the following sustainability assessment of material flows and economic sec-tors. This procedure can be repeated, starting again with a definition of bioeconomy that may change over time according to changing policies, market development and public perceptions of bioeconomy. Thus, bioeconomy monitoring considers the dynamics of the bioeconomy transition concerning processes, products, available data and connected sustainability goals. Understanding and quantifying material flows provides the foundation for comprehending the pro-cessing of biomass along value chains and final biomass uses. They also provide information for sustainability assessment. For biomass from agriculture, forests and fisheries including aquacul-ture, relevant material flows are compiled. Material flow data is not available consistently but must be collected from a broad variety of sources. Consequently, inconsistencies regarding reference units and conversion factors arise that need to be addressed further in a future monitoring. Bio-based shares of economic sectors can be quantified using mostly official statistics, but also empirical data. Bio-based shares vary considerably between economic activities. The manufacture of food products, beverages and wooden products has the highest bio-based shares. Bioeconomy target sectors like chemicals, plastics and construction still have rather small bio-based shares. The suggested assessment of sustainability effects foresees two complimentary levels of evalua-tion: material flows and economic sectors. The latter quantifies total effects of bioeconomy in a country and relates them to the whole economy or parts of it. The presented indicators were se-lected based on the Sustainability Development Goal Framework, the German Sustainable Devel-opment Strategy and the availability of data. The selection of effects and indicators to be measured in a future monitoring is a crucial point of any quantification. With sustainability being a normative concept, societal perceptions of sustainability should be taken into consideration here. In that con-text, we suggest to follow the approach of LOFASA for indicator selection. Sustainability assess-ment of material flows is demonstrated on the example of softwood lumber material flow and its core product EPAL 1 pallet using a combination of material flow analysis and life cycle assessment. Major challenges for a future monitoring of the bioeconomy’s resource base and sustainability are availability of detailed and aggregated data, identification of bio-based processes and products within the economic classifications, identification and quantification of interfaces between bio-mass types, selection of indicators for sustainability assessment and the inclusion of bio-based ser-vices.