A method and system for managing an embedded secure element (50) accessible as a slave of the resident applications (App1-3) of a host device of the eSE. The eSE includes an issuer security domain (51), ISD, with which cryptographic keys are associated. The method includes, in an application agent embedded in an OS of the host device: sending (420) the ISD a random value; receiving (435) a cryptogram corresponding to the random value encrypted using a key associated with the ISD; sending (440, 450) the random value and the cryptogram to a first extern entity entered in the application agent. The method includes: sending (455, 4555) the random value and the cryptogram from the first entity to a second external entity; verifying (4556) that the second entity possesses keys associated with the ISD from the cryptogram and the random value.