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For an undisturbed operation of two-stage high-pressure fermentation up to 100 bar, a particle-free hydrolysate appears to be necessary. This is even more important if the second stage, i.e., the methane reactor, is designed as fixed bed. Here, we present the potential of microfiltration membranes as separation unit after the first stage, which is the hydrolysis. The study included the selection of membrane material, membrane performance investigations, and long-term-behavior during the filtration period. In a series of experiments, the optimum type of membrane material and the mode of operation [either crossflow (CF) or submerged (S)] were determined. Ceramic membranes proved to be the better option to treat the process stream due to their chemical and temperature resistance. The crossflow filtration achieved a sustainable flux of up to 33 L/(m h), while long-term experiments with the submerged membranes confirmed a critical flux of 7 L/(m h). Comparative analyses of hydrolysate and permeate showed that the rejected chemical oxygen demand (COD) as well as total organic carbon (TOC) fraction and thereby the loss of organic carbon in the permeate does not reduce the methane yield.