Abstract The technological concept ensuring highly efficient co-digestion of by-products from the production of biodiesel and sewage sludge was examined. Rapeseed cakes (RC) 1–5% addition to waste activated sludge (WAS) 95–99% in digesters, positively influenced the degree of biodegradation of organic matter and the quantity and quality of the biogas produced. Under the optimal conditions (HRT = 20–22 days), the co-digestion mixtures (WAS + microwave disintegration + RC) generated double the amount of biogas, containing approximately 10–12% more CH4, than the samples which had the sewage sludge only. Under these conditions, the biogas yield increased by approximately 48–82% depending on the co-substrate used and was further improved via the introduction of microwave pre-treatment. After testing at the pilot scale, this method could be considered as a sustainable alternative to conventional methods for WAS and RC treatment.