One of the tools to attain the goal of climate-neutrality by 2050 by the European Union is increasing the share of renewable energy sources (RESs) in the energy mix of member states. A major part of the future bioenergy mix is to be played by biomass. As many hazards have been pointed out when using forest biomass, particular attention is paid to the potential of agro biomass. However, as agro biomass is sourced mostly locally, the supply may not be sufficient to meet the growing demand. Therefore, international trade (including overseas) might become increasingly important to meet the EU renewable energy targets. In this context, it is seaports that may play a major part in developing biomass supply chains. The main purpose of the article is to fill the research gap by identifying the pros and cons for the development of biomass sea-based supply chains through secondary ports and specifying their relevance from the perspective of major stakeholders in the context of decarbonization processes. The supplementary purpose of the study was the verification of the environmental sustainability of biomass sea-based supply chains through secondary ports versus land transport (carbon footprint). This study applied the single case study method (the case of the secondary port in Szczecin). The case study strategy involved qualitative and quantitative research techniques. Our research study showed that (1) overseas agro biomass (wastes and residues) may become a significant tool in the process of decarbonization of economies that are heavily reliant on coal as a transition fuel and as a stable RES in the structure of the future energy mix; and (2) biomass sea-based supply chains may be an attractive alternative for secondary ports affected by negative outcomes of decarbonization. However, a dedicated biomass terminal would make the secondary ports more attractive for this type of cargo. A biomass terminal may provide sufficient port service efficiency and enable harmonization of deliveries. Additionally, the carbon footprint analysis performed in this study has shown that biomass sea-based supply chains generate lower CO2 emissions than alternative land deliveries.