HY zeolites hydrophobized by functionalization with organosilanes are much more stable in hot liquid water than the corresponding untreated zeolites. Silylation of the zeolite increases hydrophobicity without significantly reducing the density of acid sites. This hydrophobization with organosilanes makes the zeolites able to stabilize water/oil emulsions and catalyze reactions of importance in biofuel upgrading, i.e., alcohol dehydration and alkylation of m-cresol and 2-propanol in the liquid phase, at high temperatures. While at 200 °C the crystalline structure of an untreated HY zeolite collapses in a few hours in contact with a liquid medium, the functionalized hydrophobic zeolites keep their structure practically unaltered. Detailed XRD, SEM, HRTEM, and BET analyses indicate that even after reaction under severe conditions, the hydrophobic zeolites retain their crystallinity, surface area, microporosity, and acid density. It is proposed that by preferentially anchoring hydrophobic functionalities on the external surface, the direct contact of bulk liquid water and the zeolite is hindered, thus preventing the collapse of the framework during the reaction in liquid hot water.