diff --git a/changelog.d/66.bugfix b/changelog.d/66.bugfix
new file mode 100644
index 000000000000..9547cfeddd63
--- /dev/null
+++ b/changelog.d/66.bugfix
@@ -0,0 +1 @@
+Create a mapping between user ID and threepid when binding via the internal Sydent bind API.
\ No newline at end of file
diff --git a/synapse/handlers/identity.py b/synapse/handlers/identity.py
index 558ab24a8f3c..3cf76e954ec8 100644
--- a/synapse/handlers/identity.py
+++ b/synapse/handlers/identity.py
@@ -1066,6 +1066,9 @@ async def bind_email_using_internal_sydent_api(
         Raises:
             HTTPResponseException: On a non-2xx HTTP response.
         """
+        # Extract the domain name from the IS URL as we store IS domains instead of URLs
+        id_server = urllib.parse.urlparse(id_server_url).hostname
+
         # id_server_url is assumed to have no trailing slashes
         url = id_server_url + "/_matrix/identity/internal/bind"
         body = {
@@ -1074,8 +1077,14 @@ async def bind_email_using_internal_sydent_api(
             "mxid": user_id,
         }
 
+        # Bind the threepid
         await self.http_client.post_json_get_json(url, body)
 
+        # Remember where we bound the threepid
+        await self.store.add_user_bound_threepid(
+            user_id=user_id, medium="email", address=email, id_server=id_server,
+        )
+
 
 def create_id_access_token_header(id_access_token: str) -> List[str]:
     """Create an Authorization header for passing to SimpleHttpClient as the header value
diff --git a/tests/handlers/test_register.py b/tests/handlers/test_register.py
index f5033c94fec5..e951a62a6dc0 100644
--- a/tests/handlers/test_register.py
+++ b/tests/handlers/test_register.py
@@ -566,6 +566,12 @@ def test_user_email_bound_via_sydent_internal_api(self):
             {"address": "alice@example.com", "medium": "email", "mxid": "@alice:test"},
         )
 
+        # Check that we stored a mapping of this bind
+        bound_threepids = self.get_success(
+            self.store.user_get_bound_threepids("@alice:test")
+        )
+        self.assertListEqual(bound_threepids, [{"medium": "email", "address": email}])
+
     def uia_register(self, expected_response: int, body: dict) -> FakeChannel:
         """Make a register request."""
         request, channel = self.make_request(