The catalytic deoxygenation of bio-based feedstocks to fuels and chemicals presents new challenges to the catalytic scientist, with many transformations either performed in or liberating water as a byproduct during reaction. The design of catalysts with tunable hydrophobicity to aid product and reactant adsorption or desorption, respectively, is vital for processes including (trans)esterification and condensation reactions employed in sustainable biodiesel production and bio-oil upgrading processes. Increasing surface hydrophobicity of catalyst materials offers a means to displace water from the catalyst active site, and minimizes potential deactivation or hydrolysis side reactions. Hybrid organic–inorganic porous solids offer exciting opportunities to tune surface polarity and hydrophobicity, as well as critical parameters in controlling adsorption, reactant activation, and product selectivity in liquid and vapor phase catalysis. Here, we review advances in the synthesis and application of sulfonic-acid-functionalized periodic mesoporous organosilicas (PMO) as tunable hydrophobic solid acid catalysts in reactions relevant to biorefining and biofuel production.