The invention is a method for managing a secure channel between a server and a secure element embedded in a first device, wherein a user agent embedded in a second device establishes a HTTPS session with the serverand retrievesa web application from theserver, themethod comprising the steps: -the server sends to the web applicationan application certificate which is linked to a specific data reflecting the identity of the server, -the secure element gets the application certificate and the specific data, -the secure element checks the validity of the application certificate and that the application certificate is consistently linked to the specific data, -in case of successful checks, the secure element and the server generate an ephemeral session key and use it for opening a secure channel.