The European biofuel and bioenergy industry faces increasing challenges in achieving sustainable energy production while meeting carbon neutrality targets. This study provides a detailed analysis of biogenic emissions from biofuel and bioenergy production, with a focus on key sectors such as biogas, biomethane, bioethanol, syngas, biomass combustion, and biomass pyrolysis. Over 18,000 facilities were examined, including their feedstocks, production processes, and associated greenhouse gas emissions. The results highlight forestry residues as the predominant feedstock and expose significant disparities in infrastructure and technology adoption across EU Member States. While countries like Sweden and Germany lead in emissions management and carbon capture through bioenergy production with carbon capture and storage systems (BECCS), other regions face deficiencies in bioenergy infrastructure. The findings underscore the potential of BECCS and similar carbon management technologies to achieve negative emissions and support the European Green Deal’s climate neutrality goals. This work serves as a resource for policymakers, industry leaders, and researchers, fostering informed strategies for the sustainable advancement of the biofuels sector.

Anaerobic digestion (AD) produces renewable energy but releases biogenic CO₂ and generates digestate requiring management. This paper evaluates four emerging pathways for CO₂ capture and reuse in AD systems: (1) in situ CO₂ conversion to CH₄ via microbial electrolysis cells (MECs), (2) hydrogenotrophic CO₂ methanation using green hydrogen, (3) enzymatic CO₂ capture coupled with autotrophic algae cultivation, and (4) digestate pyrolysis with syngas biomethanation. Each pathway is assessed in terms of technical feasibility, biocatalyst performance, system configuration, and key implementation challenges. Integrated scenarios demonstrate up to 98% CO₂ emission reduction, substantial bioenergy yield improvements, and enhanced nutrient and biomass recovery compared to conventional AD. MEC-based and hydrogenotrophic pathways show the highest energy efficiency, while algae-based systems provide added bioproduct valorization. The remaining limitations include cost, process integration, and scale-up. The study defines development priorities to advance zero-emission AD technologies for the agri-food and waste management sectors.