The invention is a method for managing applications in a secure element comprising a communication interface. An application is installed in the secure element and configured to be implicitly selected on the communication interface. The method comprises the following steps: —the secure element receives a command requesting the installation of a new application configured to be implicitly selected on the communication interface, —upon receipt of the command, the secure element installs the new application, configures the new application to be implicitly selected on the communication interface and keeps the previous application unchanged.