Transitioning from fossil fuels to renewable energy sources is essential for combating climate change and minimizing greenhouse gas emissions. Innovative biorefineries are at the forefront of this shift, designed for enhanced productivity and carbon neutrality. These facilities can extract low-carbon fuels and biobased materials from renewable feedstocks, presenting opportunities for diverse product development and low-carbon outputs. Recent advancements in acidogenic and methanogenic biorefineries showcase their potential to produce valuable compounds, including carboxylates, alcohols, and biopolymers while generating fuels like hydrogen and methane. This article explores biorefineries extracting low-carbon fuels and biobased materials from renewable feedstocks, emphasizing advancements in renewable fuel and chemical production. It focuses on acidogenic and methanogenic biorefineries, highlighting synergies in extracting and utilizing compounds such as carboxylates, alcohols, and biopolymers. Additionally, it addresses the production of hydrogen, methane, bioelectricity, and bio-ammonium, emphasising their role in carbon farming and the associated challenges in optimizing these processes for sustainable energy solutions.