Catalytic treating of biomass fast pyrolysis vapors offers a promising route to convert many different types of lignocellulosic biomass into biofuels. Considerable research efforts have focused on using zeolite catalysts, especially the microporous HZSM-5 zeolite. Unfortunately, the zeolite’s initial high activity in forming coke and light gases reduces the overall oil yield. In this contribution, we synthesized conventional HZSM-5 zeolite, mesoporous HZSM-5 zeolite, and a core-shell catalyst consisting of mesoporous HZSM-5 zeolite coated with a thin layer (<20 nm) of silicalite-1 zeolite. The catalysts were characterized by inductively coupled plasma optical emission spectroscopy (ICP-OES), X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), N2 and Ar physisorption, temperature programmed desorption of ammonia (NH3-TPD), diffuse reflectance infrared fourier transform spectroscopy (DRIFT) spectra, and 27Al nuclear magnetic resonance (NMR). The catalysts were tested in a tandem micro-pyrolyzer system for deoxygenation of wheat straw derived fast pyrolysis vapors in a downstream catalytic fixed bed reactor and the quantitative product analysis was performed with GC-MS/FID/TCD and TGA-MS. The change in yields of different product groups was monitored during catalyst deactivation for an increasing number of pyrolysis vapor pulses and the cumulative carbon recoveries of all product streams (char, vapors, gas, and coke) were compared at different biomass-to-catalyst ratios (∼4 and ∼1) for catalyst loadings of 2 and 8 mg, respectively. In addition, the yields were compared for the same number of zeolitic acid sites. Even though the coking propensity was highest for the mesoporous HZSM-5 (5.1% carbon recovery of fed biomass at B:C = 1), it showed improved conversion of oxygenates (wt% O of vapors = 15) and a higher tolerance towards deactivation by coking compared to the conventional HZSM-5 (wt% O of vapors = 20). Coating of mesoporous HZSM-5 with silicalite-1 reduced the number of acid sites per mass of catalyst by ∼20%, which is attributed to the addition of the inert silicalite-1 layer and passivation of the external acid sites of the mesoporous HZSM-5. Compared to mesoporous HZSM-5, the added silicalite-1 shell reduced the coke yield by 43% (from 5.1 to 2.9 wt% of fed biomass carbon) for the same catalyst mass and by 8% (4.7 wt% of fed biomass carbon) for the same total number of acid sites. Furthermore, the tolerance towards deactivation observed for the mesoporous HZSM-5 core was largely preserved—especially for conversion of small oxygenates like acids, alcohols and aldehydes, resulting in vapors with 14 wt% O.