Various embodiments of the present invention relate to incorporating an embedded secure element into a mobile device, and more particularly, to systems, devices and methods of incorporating the embedded secure element into a mobile device for identity authentication, data storage and processing in trusted transactions. These trusted transactions require a high security level to protect sensitive data or programs in bank account management, purchasing orders, contactless payment, passport verification, and many other high-security applications. The secure element will provide a root of trust such that that applications running on the mobile device are executed in a controlled and trusted environment. In addition to conventional password or encryption protection, alternative security features are introduced from both software and hardware levels based on the embedded secure element. Therefore, the security level of the mobile device is not only enhanced, but also may potentially exceed that of the conventional POS terminals.