Applications are stored on removable storage of a mobile device in an encrypted form to provide isolation and piracy protection. In one implementation, each application is encrypted using its own associated encryption key that is generated based on an identifier of the application and a master key that is associated with a trusted platform module of the mobile device. In another implementation, each application is encrypted using two associated encryption keys. One key is used to encrypt binary data associated with the application such as source code, and the other key is used to encrypt application data such as graphics and configuration files. The encryption keys are each generated using the identifier of the application, the master key, and identifiers of the folders where the corresponding data types are stored on the mobile device. The removable storage includes SD cards formatted using the FAT or exFAT file systems.