Authentication method of at least one application using resources stored in a security module associated to an equipment connected to a control server via a network. The control server receives via the network, analyses and verifies identification data comprising at least an identifier of the equipment and an identifier of the security module, generates a cryptogram comprising a digest of the application, the identification data and instructions intended for the security module and transmits the cryptogram, via the network and the equipment, to the security module. The latter verifies the application by comparing the digest extracted from the cryptogram with a calculated digest, wherein, during at least one of initialization and activation of the application, the security module executes the instructions extracted from the cryptogram and either releases or blocks access to certain resources of said security module according to a result of the verification of the application.