This paper presents the study concerning the impact of the basic operational parameters on the performance of an innovative microfiltration membrane reactor applied for enzymatic hydrolysis of lignocellulosic biomass. The concept and basic hydrodynamics of the reactor with tubular ceramic membranes and a propeller agitator were shown. Besides, the efficiency of enzymatic hydrolysis of corn straw was studied to check reactor functionality. It has been proven that the proposed reactor construction can improve the microfiltration of lignocellulosic suspension by reducing the cake layer on the membrane surface. Increasing the rotational speed of the propeller agitator also improved the filtration efficiency. The permeate flux during the microfiltration experiments was lower for smaller lignocellulose biomass fraction (D < 425 μm) when compared to the less fragmented corn straw (425 < D < 900 μm). For larger solid fractions, a stirring speed increase enhanced the separation efficiency regardless of the differences in biomass concentration. In contrast, this trend for the finer biomass fraction was only noticeable for the highest used biomass concentration (C = 2.0%). Considering the enzymatic hydrolysis of corn straw, membrane separation of reaction products positively influenced the process yield, and the results depended on the applied operational parameters.