diff --git a/synapse/rest/client/v2_alpha/register.py b/synapse/rest/client/v2_alpha/register.py
index dc3e265bcd..ecec610859 100644
--- a/synapse/rest/client/v2_alpha/register.py
+++ b/synapse/rest/client/v2_alpha/register.py
@@ -391,13 +391,6 @@ class RegisterRestServlet(RestServlet):
         # the user-facing checks will probably already have happened in
         # /register/email/requestToken when we requested a 3pid, but that's not
         # guaranteed.
-        #
-        # Also check that we're not trying to register a 3pid that's already
-        # been registered.
-        #
-        # This has probably happened in /register/email/requestToken as well,
-        # but if a user hits this endpoint twice then clicks on each link from
-        # the two activation emails, they would register the same 3pid twice.
 
         if auth_result:
             for login_type in [LoginType.EMAIL_IDENTITY, LoginType.MSISDN]:
@@ -413,17 +406,6 @@ class RegisterRestServlet(RestServlet):
                             Codes.THREEPID_DENIED,
                         )
 
-                    existingUid = yield self.store.get_user_id_by_threepid(
-                        medium, address,
-                    )
-
-                    if existingUid is not None:
-                        raise SynapseError(
-                            400,
-                            "%s is already in use" % medium,
-                            Codes.THREEPID_IN_USE,
-                        )
-
         if registered_user_id is not None:
             logger.info(
                 "Already registered user ID %r for this session",
@@ -446,6 +428,28 @@ class RegisterRestServlet(RestServlet):
             if auth_result:
                 threepid = auth_result.get(LoginType.EMAIL_IDENTITY)
 
+                # Also check that we're not trying to register a 3pid that's already
+                # been registered.
+                #
+                # This has probably happened in /register/email/requestToken as well,
+                # but if a user hits this endpoint twice then clicks on each link from
+                # the two activation emails, they would register the same 3pid twice.
+                for login_type in [LoginType.EMAIL_IDENTITY, LoginType.MSISDN]:
+                    if login_type in auth_result:
+                        medium = auth_result[login_type]['medium']
+                        address = auth_result[login_type]['address']
+
+                        existingUid = yield self.store.get_user_id_by_threepid(
+                            medium, address,
+                        )
+
+                        if existingUid is not None:
+                            raise SynapseError(
+                                400,
+                                "%s is already in use" % medium,
+                                Codes.THREEPID_IN_USE,
+                            )
+
             (registered_user_id, _) = yield self.registration_handler.register(
                 localpart=desired_username,
                 password=new_password,