Most conventional digesters used for animal wastewater treatment include continuously stirred-tank reactors. While imperfect mixing patterns are more common than ideal ones in real reactors, anaerobic digestion models often assume complete mixing conditions. Therefore, their applicability appears to be limited. In this study, a mathematical model for anaerobic digestion of cattle manure was developed to describe the dynamic behavior of non-ideal mixing continuous flow reactors. The microbial kinetic model includes an enzymatic hydrolysis step and four microbial growth steps, together with the effects of substrate inhibition, pH and thermodynamic considerations. The biokinetic expressions were linked to a simple two-region liquid mixing model, which considered the reactor volume in two separate sections, the flow-through and the retention regions. Deviations from an ideal completely mixed regime were represented by changing the relative volume of the flow-through region (a) and the ratio of the internal exchange flow rate to the feed flow rate (b). The effects of the hydraulic retention time, the composition of feed, the initial conditions of the reactor and the degree of mixing on process performance can be evaluated by the dynamic model. The simulation results under different conditions showed that deviations from the ideal mixing regime decreased the methane yield and resulted in a reduced performance of the anaerobic reactors. The evaluation of the impact of the characteristic mixing parameters (a) and (b) on the anaerobic digestion of cattle manure showed that both liquid mixing parameters had significant effects on reactor performance.