One way to mitigate the negative impacts of climate change, is for society to move towards a biobased economy, where fossil resources are replaced by biobased ones. This replacement requires the development of biobased supply chains that differ significantly from the conventional supply chain. For example, seasonality and variability of the feedstocks create specific challenges for biobased systems and call for customized solutions for the design and operation of biobased chains. As a result, the modelling efforts to support decision-making processes for biobased logistics and supply chains have some different requirements. This paper presents a systematic literature review on logistics and supply chain modelling studies for the biobased economy published in a period of 2011–2020. The literature analysis shows that most modelling studies for the biobased economy are strategic optimization models aiming to minimize economic impact. As biomass source, forest and agricultural residues are mostly used, and fuel and energy are the most common biobased applications. Modelling strategies, biomass sources and applications are however diversifying, which is what we encourage for future research. Also, not only focusing on economic optimization but also optimizing social and environmental performance is an important future research direction, to deal with the sustainability challenges the world is facing.