Methods, systems, and media for detecting covert malware are provided. In accordance with some embodiments, a method for detecting covert malware in a computing environment is provided, the method comprising: receiving a first set of user actions; generating a second set of user actions based on the first set of user actions and a model of user activity; conveying the second set of user actions to an application inside the computing environment; determining whether state information of the application matches an expected state after the second set of user actions is conveyed to the application; and determining whether covert malware is present in the computing environment based at least in part on the determination.