Application customization

Methods and systems for customizing applications in enterprise mobility management systems are described herein. A client agent software application on a mobile device may be customized to embed or make available enterprise server URLs, a session cookie for authentication, and various other data during the device enrollment process. The customization of the client agent may be based on the device, user, and/or enrollment session. After the device is enrolled in the enterprise system, the embedded data may be accessed by the client agent application to support seamless single-sign-on during first-time use. Additional customized applications based on device, user, and/or enrollment session, may be generated and provided to mobile devices during or after device enrollment. Customized applications may be based on application templates, such as packaged web applications or specific implementations of hosted applications.