An optimizer controller controls a hypervisor optimizer to regulate operation of the optimizer to insure the optimizer does not negatively impact operation of software applications. The optimizer controller monitors applications and application performance to determine whether to turn on or off specific optimization features for specific applications. The optimizer may also notify a user of potential problems. The optimizer controller may utilize optimization rules for specific applications that set the conditions for controlling the optimizer. The rules may be dynamically changed based on observed performance and trends of the applications.