The conversion of biomass-derived oxygenates over zeolite catalysts constitutes a challenge for the efficient production of bio-based chemicals and fuels due to difficulty in controlling the selectivity and high coke formation of such reactions. This is partly attributed to the microstructure of zeolite catalyst which affects the conversion and selectivity of products derived from biomass-derived oxygenates. In this study, the conversion and deactivation characteristics of three different model oxygenates found in biomass bio-oil (namely, acetol, furfural and guaiacol) over ZSM-5 zeolites of varying acidity, pore and crystal size prepared with bottom-up and top-down approaches were evaluated using a fixed bed microreactor at atmospheric pressure and a space velocity of 5 h−1 at a temperature range of 450–650 °C. Analysis of the experimental results indicates that the optimum temperature for such conversions is in the vicinity of 600 °C allowing for complete conversion of the compounds and high resistance to coking. The mechanisms of those conversions are discussed based on the obtained results. In general, crystal size and mesoporosity induce easier access to active sites improving mass transfer but also alter the location type, and strength of acid sites allowing for higher yields of primary and intermediate products such as olefins.