Purpose <p>This study examines the potential of anaerobic co-digestion of microalgal biomass with carbon-rich wastes to improve CH₄ yield and support sustainable digestate valorization.</p> Methods <p>The green microalga <i>Desmodesmus intermedius</i> KNUA024 was cultivated under controlled conditions and tested in biochemical methane potential assays, either alone or with waste cooking oil (WCO) as a co-substrate. Microbial communities were profiled by high-throughput sequencing, and digestates were analyzed for nutrients and trace metals.</p> Results <p>Co-digestion with WCO increased CH₄ yield by up to 47% compared to microalgae-only digestion and improved process stability. Substrate composition strongly influenced microbial succession, with lipid-rich substrates promoting syntrophic and methanogenic groups. Digestates contained valuable nutrients but also trace metals near regulatory limits, indicating the need for careful monitoring.</p> Conclusion <p>Substrate-driven microbial dynamics play a decisive role in both methane production and digestate quality. Co-digestion with lipid-rich wastes offers a practical strategy to enhance anaerobic digestion efficiency and contribute to sustainable bioenergy systems.</p> Statement of Novelty <p>This study integrates three-domain (bacterial, archaeal, and fungal) microbial profiling with digestate valorization, linking enhanced biogas production to sustainable reuse pathways and offering a novel approach toward a circular bioeconomy in microalgae-based waste management.</p>