<p>Anaerobic co-digestion (ACoD) of organic waste is an effective biotechnology for waste management, biogas production, and fertilizer generation. Agitation speed plays a crucial role in substrate mixing, nutrient transfer, and microbial activity. On the one hand, insufficient agitation can hinder homogeneous heat and nutrient distribution, creating dead zones. On the other hand, excessive agitation increases shear forces, destabilizing floc formation and inducing microbial stress, negatively affecting system performance. Additionally, agitation speed impacts treatment plant operational costs. This study evaluated three agitation speeds (30, 60, and 80&#xa0;r/min) in ACoD of sewage sludge (SS) and the organic fraction of municipal solid waste (OFMSW) using 1&#xa0;m³ reactors. The methodology included substrate characterization, physicochemical parameter monitoring, methane (CH₄) quantification, organic matter removal, pathogenic microorganism inhibition, and heavy metal speciation. The results showed that a 30&#xa0;r/min agitation speed optimized CH₄ production (1048.51&#xa0;mL/g VS) and enhanced process stability. Higher agitation speeds significantly reduced performance. The modified Gompertz model exhibited the best fit for CH₄ prediction. Moreover, lower agitation speeds favored fertilizer production with agricultural potential, promoting nutrient transformation while effectively inhibiting pathogenic microorganisms without posing health or environmental risks. Optimizing agitation speed is crucial for maximizing biogas production in ACoD of SS and OFMSW, with significant industrial-scale implications.</p> Graphical abstract <p></p>