The effect of slurry mixing in an anaerobic digester on biogas production was intensively studied in the last few years. This subject is still debatable due to fact that this process involves three phases, solid-gas-liquid, along with the involvement of microbes during biochemical reactions, which are highly vulnerable to changes in hydrodynamic shear stresses and mixing conditions. Moreover, the complexity in the direction of optimization of mixing magnifies due to the implication of both fluid mechanics and biochemical engineering to study the effect of mixing in anaerobic digestion (AD). The effect of mixing on AD is explored using recent literature and theoretical analysis, concentrating on the multi-phase and multi-scale aspects of AD. The tools and methods available to experimentally quantify the function of mixing on both the global and local scales are summarized in this study. The major challenge for mixing in an anaerobic digester is to minimize dead zones and maintain uniform distribution of viscosity and shear at low mixing intensities without disrupting the microbial flocs and syntrophic relationships between the bacteria during the AD process. This study is a critical analysis of various techniques and approaches adopted by researchers to evaluate the effectiveness of mixing regimes and mixing equipment. Most studies describe biogas production performance and hydrodynamic characteristics of the digesters separately, but the evaluation of mixing requires interdisciplinary experts, which include mechanical engineers, microbiologists and hydrodynamic experts. Through this review, the readers will be guided through intensive literature regarding agitation, the best possible way to scrutinize the agitation problems and the approach to answering the question “why is the optimization of mixing in an anaerobic digester still a debatable subject?”.