This study adapts the biphasic OrganoCat system into a flow‐through (FT) reactor, using a heated tubular setup where a mixture of oxalic acid and 2‐methyltetrahydrofuran (2‐MTHF) is pumped through beech wood biomass. This method minimizes solvent‐biomass contact time, facilitating rapid product removal and reducing the risk of secondary reactions. A comparative analysis with traditional batch processes reveals that the FT system, especially under severe conditions, significantly enhances extraction efficiency, yielding higher amounts of lignin and sugars with reduced solid residue. Notably, the FT system shows partial hydrolysis of the cellulose, which increases with temperature while not producing significant amounts of furfural or 5‐HMF, indicating more efficient depolymerization of polysaccharides without substantial sugar degradation. A statistical design of experiments (DOE) using a Box‐Behnken design elucidates the influence of process variables (time, solvent flow rate, temperature) on the yield. Key findings highlight reactor temperature as the dominant factor affecting yields, with process time showing a significant but less pronounced impact. This study demonstrates the potential of the FT OrganoCat system for efficient lignocellulosic biomass fractionation and represents an advancement towards continuous lignocellulose processing, contributing to our knowledge of process optimization for improved biorefinery applications.