In Flask, session security works by sending a signed cookie to the user that stores session data. When a user sends a request, Flask checks if the session cookie exists and if it is valid. If valid, the server allows the request and can access session data like the logged-in user. If invalid or missing, the server rejects or clears the session to protect security. Setting app.secret_key is essential to sign cookies and prevent tampering. When a user logs out, the session is cleared to remove sensitive data. This process ensures user sessions are safe and trusted.