Disclosed are systems and methods for altering a functionality of an application installed in a computer. In one aspect, an exemplary method comprises, by a hardware processor of the computer, receiving an application update to the application, wherein the application update comprises one or more of a patch, service pack and software update, updating the application based on the application update by applying the application update to the application, detecting one or more events occurring on a computer after the updating of the application based on the application update, determining one or more portions of the application which caused the one or more events to occur on the computer, and altering the one or more portions of the application when a number of detected events exceeds a threshold, wherein how the one or more portions are altered depends on the one or more events.