Systems and methods for securely managing biometric data are provided. In a method conducted at a secure element which is directly connected to a biometric input, biometric data is received directly from the biometric input. A biometric signature based on the biometric data is obtained. A seed value specific to the biometric data is accessed by obtaining the seed value from the biometric data or biometric signature. The biometric signature is encoded using an obscured algorithm and the seed value to generate a token which is output for secure storage within the secure element or secure transmission to a secure server for registration or authentication of the biometric data. Obtaining the seed value from the biometric data or biometric signature can be repeated reliably to obtain the same the seed value