Aimed at comparing the single-stage and two-stage co-digestion of end-of-life dairy products (EoL-DPs) with a mixture of agro-industrial waste(water)s. The two systems were operated in parallel and operational parameters including hydraulic retention time (HRT) and organic loading rate were tested for their effect on bio-hydrogen and bio-methane production. During acidogenic fermentation of EoL-DPs, HRT of 3 days led to process instability due to lactate accumulation, whereas HRT of 6 days resulted in maximum hydrogen yield of 0.676 mol H2 mol−1 carbohydrates consumed. Slaughterhouse waste pasteurization did not significantly affect the anaerobic digestion (AD) process, while the increased EoL-DPs feeding ratio enhanced methane yield in both systems (34.7–37.6% increase). Interestingly, the high ammonia concentration (c.a. 4 g L−1) did not inhibit AD. The energy productivity of the two-stage system was roughly 30% higher, and therefore is the suggested approach for agro-industrial waste(water) valorization.