Process simplification by integrating Fischer-Tropsch synthesis (FTS) with hydrocracking (HC) in a microstructured reactor was studied experimentally and by modeling and simulation. A simplified model was created to investigate the experimentally observed FTS and HC performance in the presence of larger amounts of liquid. It is assumed that part of the catalyst would be blocked if the liquid fraction exceeds a threshold. The liquid blocking would cause enlarged diffusion resistance or even inaccessible regions in the catalyst bed, particularly in microstructured reactors with broad flat channels such as the annular geometry of this study. Significant mass transfer limitation was observed for Fischer Tropsch synthesis in the assumed liquid-filled spots. Hydrocracking exhibits limited response to internal diffusion limitation. Good agreement with experimental data was obtained here by assuming inaccessible local regions in the packed bed. Identical cross section-averaged effectiveness factors of 0.6-0.7 were obtained for the liquid-filled sections in both FTS and HC.