Hierarchical zeolites have been identified as special catalytic materials with improved catalytic properties. In this study, hierarchical bifunctional ZSM5 based catalysts were prepared by desilication for controlled mesoporosity development and have been modified by Co doping. Their performance in the catalytic pyrolysis of oak in a lab scale reactor was evaluated. Desilicated counterparts were proven more active in deoxygenation of bio oil, while carbon deposition on the catalysts reduced compared to non-desilicated counterparts. Increased Lewis acidity favors decarboxylation reactions, while higher olefins as well as PAH content indicate easier diffusion within and from the porous network and interactions in the mesopores. The conversion of bulky lignin molecules (alkoxy phenols) is enhanced by the mesopores, while acidity is of secondary importance. Coke deposition inside the pores is more profound in the desilicated catalysts due to larger pore size. Carbon deposition on the catalysts is reduced in the following order: HZSM5 > Co/HZSM5 > Ds-HZSM5 > Co/Ds-HZSM5. GC–MS characterization of the CH2Cl2 soluble coke indicated that for the desilicated counterparts the main coke precursors are the bulky lignin molecules which are partially deoxygenated.