Method for deploying an application in a secure element of a communication terminal comprising a non-secure processing unit executing a program for calling the applications of the secure element; the method comprising the step of transferring, via at least one communication network, data between a first trusted server associated with a provider of the secure element so as to execute a first program for managing the security element, a second trusted server associated with at least one applications provider so as to execute a program for managing applications of the secure element, and the communication terminal, so as to create, in the secure element, a secure domain and install the application therein; characterized in that the method comprises the steps of: - establishing a first exchange of data between the applications provider and the calling program so as to obtain an application installation authorization; and, if the installation is authorized, - establishing a second exchange of data between the first management program and the calling program so as to create the secure domain in the secure element and transfer a key for access to the secure domain to the calling program, - establishing a third exchange of data between the second management program and the calling program so as to transfer the access key to the second management program and have the second management program download and install the application in the secure domain, - having the first management program, before transferring it to the calling program, encrypt the key for access to the secure domain with an intermediate encryption key known to the second management program or having the second management program modify the key for access to the secure domain as soon as the key is received, so as to prohibit the use of the access key by any other than the second management program just after the second manager program has taken possession of the key before the downloading of the application into the secure domain. - establishing a first exchange of data between the applications provider and the calling program so as to obtain an application installation authorization; and, if the installation is authorized, - establishing a second exchange of data between the first management program and the calling program so as to create the secure domain in the secure element and transfer a key for access to the secure domain to the calling program, - establishing a third exchange of data between the second management program and the calling program so as to transfer the access key to the second management program and have the second management program download and install the application in the secure domain, - having the first management program, before transferring it to the calling program, encrypt the key for access to the secure domain with an intermediate encryption key known to the second management program or having the second management program modify the key for access to the secure domain as soon as the key is received, so as to prohibit the use of the access key by any other than the second management program just after the second manager program has taken possession of the key before the downloading of the application into the secure domain.