This study carried out an anaerobic co-digestion treatment of cheese whey using cattle manure as a co-substrate. A co-digestion process was implemented in three tubular reactors, each one with a different organic load rate (0.5, 1.0 and 1.5 kg CODfed m?3digester day?1). A biochemical and microbiological analysis along the axial axis of each reactor showed that it was possible to obtain a phase separation with an organic load rate of 1.0 kg CODfed m?3digester day?1. The volatile fatty acid production phase takes place in the first reactor section and the consumption phase in the second section. Results from high-throughput sequencing analysis showed differences in the microbial communities between the samples of the three reactors for both eubacterial and archaeal compositions. In the reactor with intermediate organic loading rate, acetoclastic communities predominate, while at lower load, both acetoclastic and hydrogenotrophic communities are detected. Additionally, a microbial consortium stratification was observed.