diff --git a/changelog.d/5586.bugfix b/changelog.d/5586.bugfix
new file mode 100644
index 0000000000..c0b1ecf81a
--- /dev/null
+++ b/changelog.d/5586.bugfix
@@ -0,0 +1 @@
+Fixed m.login.jwt using unregistred user_id and added pyjwt>=1.6.4 as jwt conditional dependencies. Contributed by Pau Rodriguez-Estivill.
diff --git a/synapse/rest/client/v1/login.py b/synapse/rest/client/v1/login.py
index ede6bc8b1e..e88d2ad7bd 100644
--- a/synapse/rest/client/v1/login.py
+++ b/synapse/rest/client/v1/login.py
@@ -319,12 +319,12 @@ class LoginRestServlet(RestServlet):
             raise LoginError(401, "Invalid JWT", errcode=Codes.UNAUTHORIZED)
 
         user_id = UserID(user, self.hs.hostname).to_string()
+        device_id = login_submission.get("device_id")
+        initial_display_name = login_submission.get("initial_device_display_name")
 
         auth_handler = self.auth_handler
         registered_user_id = yield auth_handler.check_user_exists(user_id)
         if registered_user_id:
-            device_id = login_submission.get("device_id")
-            initial_display_name = login_submission.get("initial_device_display_name")
             device_id, access_token = yield self.registration_handler.register_device(
                 registered_user_id, device_id, initial_display_name
             )
@@ -338,11 +338,8 @@ class LoginRestServlet(RestServlet):
             user_id, access_token = (
                 yield self.registration_handler.register(localpart=user)
             )
-
-            device_id = login_submission.get("device_id")
-            initial_display_name = login_submission.get("initial_device_display_name")
             device_id, access_token = yield self.registration_handler.register_device(
-                registered_user_id, device_id, initial_display_name
+                user_id, device_id, initial_display_name
             )
 
             result = {