Anaerobic digestion of cheese whey offers a two-fold benefit: reduction of pollution potential and biogas production. Usually effective anaerobic digestion of acid whey is hindered by low pH (~ 4.5) and low buffer capacity of the substrate. The aim of this study was to evaluate the process of acid cheese whey anaerobic digestion with respect to changes in microbial population dynamics and effective biogas production. The results showed that it is possible to obtain high methane yields (176–278Lkg-1VS-1) in a system with high organic loading rates (till 4.9 VS m-3 day) and no apparent acid inhibition on methanogenic microbial population. Moreover, Archaea population showed the ability to rapidly adapt and actively convert the substrate.