diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 839b895c82..4c7b0335e6 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -8,21 +8,21 @@
 # If ignoring a pull request that was not squash merged, only the merge
 # commit needs to be put here. Child commits will be resolved from it.
 
-# Run black (#3679).
+# Run black (https://github.com/matrix-org/synapse/pull/3679).
 8b3d9b6b199abb87246f982d5db356f1966db925
 
-# Black reformatting (#5482).
+# Black reformatting (https://github.com/matrix-org/synapse/pull/5482).
 32e7c9e7f20b57dd081023ac42d6931a8da9b3a3
 
-# Target Python 3.5 with black (#8664).
+# Target Python 3.5 with black (https://github.com/matrix-org/synapse/pull/8664).
 aff1eb7c671b0a3813407321d2702ec46c71fa56
 
-# Update black to 20.8b1 (#9381).
+# Update black to 20.8b1 (https://github.com/matrix-org/synapse/pull/9381).
 0a00b7ff14890987f09112a2ae696c61001e6cf1
 
-# Convert tests/rest/admin/test_room.py to unix file endings (#7953).
+# Convert tests/rest/admin/test_room.py to unix file endings (https://github.com/matrix-org/synapse/pull/7953).
 c4268e3da64f1abb5b31deaeb5769adb6510c0a7
 
-# Update black to 23.1.0 (#15103)
+# Update black to 23.1.0 (https://github.com/matrix-org/synapse/pull/15103)
 9bb2eac71962970d02842bca441f4bcdbbf93a11
 
diff --git a/changelog.d/16637.misc b/changelog.d/16637.misc
new file mode 100644
index 0000000000..f5068ac291
--- /dev/null
+++ b/changelog.d/16637.misc
@@ -0,0 +1 @@
+Improve references to GitHub issues.
diff --git a/debian/changelog b/debian/changelog
index cbfcb8f44d..5470f3877f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1637,7 +1637,7 @@ matrix-synapse-py3 (0.99.3.1) stable; urgency=medium
 matrix-synapse-py3 (0.99.3) stable; urgency=medium
 
   [ Richard van der Hoff ]
-  * Fix warning during preconfiguration. (Fixes: #4819)
+  * Fix warning during preconfiguration. (Fixes: https://github.com/matrix-org/synapse/issues/4819)
 
   [ Synapse Packaging team ]
   * New synapse release 0.99.3.
diff --git a/pyproject.toml b/pyproject.toml
index df132c0236..825ff73f95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -192,7 +192,7 @@ phonenumbers = ">=8.2.0"
 # we use GaugeHistogramMetric, which was added in prom-client 0.4.0.
 prometheus-client = ">=0.4.0"
 # we use `order`, which arrived in attrs 19.2.0.
-# Note: 21.1.0 broke `/sync`, see #9936
+# Note: 21.1.0 broke `/sync`, see https://github.com/matrix-org/synapse/issues/9936
 attrs = ">=19.2.0,!=21.1.0"
 netaddr = ">=0.7.18"
 # Jinja 2.x is incompatible with MarkupSafe>=2.1. To ensure that admins do not
@@ -357,7 +357,7 @@ commonmark = ">=0.9.1"
 pygithub = ">=1.55"
 # The following are executed as commands by the release script.
 twine = "*"
-# Towncrier min version comes from #3425. Rationale unclear.
+# Towncrier min version comes from https://github.com/matrix-org/synapse/pull/3425. Rationale unclear.
 towncrier = ">=18.6.0rc1"
 
 # Used for checking the Poetry lockfile
@@ -377,8 +377,9 @@ furo = ">=2022.12.7,<2024.0.0"
 
 [build-system]
 # The upper bounds here are defensive, intended to prevent situations like
-# #13849 and #14079 where we see buildtime or runtime errors caused by build
-# system changes.
+# https://github.com/matrix-org/synapse/issues/13849 and
+# https://github.com/matrix-org/synapse/issues/14079 where we see buildtime or
+# runtime errors caused by build system changes.
 # We are happy to raise these upper bounds upon request,
 # provided we check that it's safe to do so (i.e. that CI passes).
 requires = ["poetry-core>=1.1.0,<=1.7.0", "setuptools_rust>=1.3,<=1.8.1"]
diff --git a/synapse/app/generic_worker.py b/synapse/app/generic_worker.py
index f7c80eee21..bcfb7a7200 100644
--- a/synapse/app/generic_worker.py
+++ b/synapse/app/generic_worker.py
@@ -104,8 +104,8 @@ logger = logging.getLogger("synapse.app.generic_worker")
 
 
 class GenericWorkerStore(
-    # FIXME(#3714): We need to add UserDirectoryStore as we write directly
-    # rather than going via the correct worker.
+    # FIXME(https://github.com/matrix-org/synapse/issues/3714): We need to add
+    # UserDirectoryStore as we write directly rather than going via the correct worker.
     UserDirectoryStore,
     StatsStore,
     UIAuthWorkerStore,
diff --git a/synapse/federation/sender/__init__.py b/synapse/federation/sender/__init__.py
index 7980d1a322..948fde6658 100644
--- a/synapse/federation/sender/__init__.py
+++ b/synapse/federation/sender/__init__.py
@@ -581,14 +581,14 @@ class FederationSender(AbstractFederationSender):
                                 "get_joined_hosts", str(sg)
                             )
                             if destinations is None:
-                                # Add logging to help track down #13444
+                                # Add logging to help track down https://github.com/matrix-org/synapse/issues/13444
                                 logger.info(
                                     "Unexpectedly did not have cached destinations for %s / %s",
                                     sg,
                                     event.event_id,
                                 )
                         else:
-                            # Add logging to help track down #13444
+                            # Add logging to help track down https://github.com/matrix-org/synapse/issues/13444
                             logger.info(
                                 "Unexpectedly did not have cached prev group for %s",
                                 event.event_id,
diff --git a/synapse/handlers/federation_event.py b/synapse/handlers/federation_event.py
index 0cc8e990d9..ba6b94a8b7 100644
--- a/synapse/handlers/federation_event.py
+++ b/synapse/handlers/federation_event.py
@@ -748,7 +748,7 @@ class FederationEventHandler:
         # fetching fresh state for the room if the missing event
         # can't be found, which slightly reduces our security.
         # it may also increase our DAG extremity count for the room,
-        # causing additional state resolution?  See #1760.
+        # causing additional state resolution?  See https://github.com/matrix-org/synapse/issues/1760.
         # However, fetching state doesn't hold the linearizer lock
         # apparently.
         #
diff --git a/synapse/handlers/presence.py b/synapse/handlers/presence.py
index 202beee738..4137fd50b1 100644
--- a/synapse/handlers/presence.py
+++ b/synapse/handlers/presence.py
@@ -1816,7 +1816,7 @@ class PresenceEventSource(EventSource[int, UserPresenceState]):
                 # the same token repeatedly.
                 #
                 # Hence this guard where we just return nothing so that the sync
-                # doesn't return. C.f. #5503.
+                # doesn't return. C.f. https://github.com/matrix-org/synapse/issues/5503.
                 return [], max_token
 
             # Figure out which other users this user should explicitly receive
diff --git a/synapse/handlers/sync.py b/synapse/handlers/sync.py
index 2f1bc5a015..bf0106c6e7 100644
--- a/synapse/handlers/sync.py
+++ b/synapse/handlers/sync.py
@@ -399,7 +399,7 @@ class SyncHandler:
         #
         # If that happens, we mustn't cache it, so that when the client comes back
         # with the same cache token, we don't immediately return the same empty
-        # result, causing a tightloop. (#8518)
+        # result, causing a tightloop. (https://github.com/matrix-org/synapse/issues/8518)
         if result.next_batch == since_token:
             cache_context.should_cache = False
 
@@ -1003,7 +1003,7 @@ class SyncHandler:
                     # always make sure we LL ourselves so we know we're in the room
                     # (if we are) to fix https://github.com/vector-im/riot-web/issues/7209
                     # We only need apply this on full state syncs given we disabled
-                    # LL for incr syncs in #3840.
+                    # LL for incr syncs in https://github.com/matrix-org/synapse/pull/3840.
                     # We don't insert ourselves into `members_to_fetch`, because in some
                     # rare cases (an empty event batch with a now_token after the user's
                     # leave in a partial state room which another local user has
diff --git a/synapse/handlers/user_directory.py b/synapse/handlers/user_directory.py
index 75717ba4f9..3c19ea56f8 100644
--- a/synapse/handlers/user_directory.py
+++ b/synapse/handlers/user_directory.py
@@ -184,8 +184,8 @@ class UserDirectoryHandler(StateDeltasHandler):
         """Called to update index of our local user profiles when they change
         irrespective of any rooms the user may be in.
         """
-        # FIXME(#3714): We should probably do this in the same worker as all
-        # the other changes.
+        # FIXME(https://github.com/matrix-org/synapse/issues/3714): We should
+        # probably do this in the same worker as all the other changes.
 
         if await self.store.should_include_local_user_in_dir(user_id):
             await self.store.update_profile_in_user_dir(
@@ -194,8 +194,8 @@ class UserDirectoryHandler(StateDeltasHandler):
 
     async def handle_local_user_deactivated(self, user_id: str) -> None:
         """Called when a user ID is deactivated"""
-        # FIXME(#3714): We should probably do this in the same worker as all
-        # the other changes.
+        # FIXME(https://github.com/matrix-org/synapse/issues/3714): We should
+        # probably do this in the same worker as all the other changes.
         await self.store.remove_from_user_dir(user_id)
 
     async def _unsafe_process(self) -> None:
diff --git a/synapse/http/matrixfederationclient.py b/synapse/http/matrixfederationclient.py
index 08c7fc1631..d5013e8e97 100644
--- a/synapse/http/matrixfederationclient.py
+++ b/synapse/http/matrixfederationclient.py
@@ -465,7 +465,7 @@ class MatrixFederationHttpClient:
         """Wrapper for _send_request which can optionally retry the request
         upon receiving a combination of a 400 HTTP response code and a
         'M_UNRECOGNIZED' errcode. This is a workaround for Synapse <= v0.99.3
-        due to #3622.
+        due to https://github.com/matrix-org/synapse/issues/3622.
 
         Args:
             request: details of request to be sent
@@ -958,9 +958,9 @@ class MatrixFederationHttpClient:
                 requests).
             try_trailing_slash_on_400: True if on a 400 M_UNRECOGNIZED
                 response we should try appending a trailing slash to the end
-                of the request. Workaround for #3622 in Synapse <= v0.99.3. This
-                will be attempted before backing off if backing off has been
-                enabled.
+                of the request. Workaround for https://github.com/matrix-org/synapse/issues/3622
+                in Synapse <= v0.99.3. This will be attempted before backing off if
+                backing off has been enabled.
             parser: The parser to use to decode the response. Defaults to
                 parsing as JSON.
             backoff_on_all_error_codes: Back off if we get any error response
@@ -1155,7 +1155,8 @@ class MatrixFederationHttpClient:
 
             try_trailing_slash_on_400: True if on a 400 M_UNRECOGNIZED
                 response we should try appending a trailing slash to the end of
-                the request. Workaround for #3622 in Synapse <= v0.99.3.
+                the request. Workaround for https://github.com/matrix-org/synapse/issues/3622
+                in Synapse <= v0.99.3.
 
             parser: The parser to use to decode the response. Defaults to
                 parsing as JSON.
@@ -1250,7 +1251,8 @@ class MatrixFederationHttpClient:
 
             try_trailing_slash_on_400: True if on a 400 M_UNRECOGNIZED
                 response we should try appending a trailing slash to the end of
-                the request. Workaround for #3622 in Synapse <= v0.99.3.
+                the request. Workaround for https://github.com/matrix-org/synapse/issues/3622
+                in Synapse <= v0.99.3.
 
             parser: The parser to use to decode the response. Defaults to
                 parsing as JSON.
diff --git a/synapse/module_api/callbacks/third_party_event_rules_callbacks.py b/synapse/module_api/callbacks/third_party_event_rules_callbacks.py
index ecaeef3511..7419785aff 100644
--- a/synapse/module_api/callbacks/third_party_event_rules_callbacks.py
+++ b/synapse/module_api/callbacks/third_party_event_rules_callbacks.py
@@ -295,7 +295,8 @@ class ThirdPartyEventRulesModuleApiCallbacks:
                 raise
             except SynapseError as e:
                 # FIXME: Being able to throw SynapseErrors is relied upon by
-                # some modules. PR #10386 accidentally broke this ability.
+                # some modules. PR https://github.com/matrix-org/synapse/pull/10386
+                # accidentally broke this ability.
                 # That said, we aren't keen on exposing this implementation detail
                 # to modules and we should one day have a proper way to do what
                 # is wanted.
diff --git a/synapse/storage/databases/__init__.py b/synapse/storage/databases/__init__.py
index 7aa24ccf21..b57e260fe0 100644
--- a/synapse/storage/databases/__init__.py
+++ b/synapse/storage/databases/__init__.py
@@ -45,7 +45,7 @@ class Databases(Generic[DataStoreT]):
     """
 
     databases: List[DatabasePool]
-    main: "DataStore"  # FIXME: #11165: actually an instance of `main_store_class`
+    main: "DataStore"  # FIXME: https://github.com/matrix-org/synapse/issues/11165: actually an instance of `main_store_class`
     state: StateGroupDataStore
     persist_events: Optional[PersistEventsStore]
 
diff --git a/synapse/storage/databases/main/events_bg_updates.py b/synapse/storage/databases/main/events_bg_updates.py
index 9c46c5d7bd..0c91f19c8e 100644
--- a/synapse/storage/databases/main/events_bg_updates.py
+++ b/synapse/storage/databases/main/events_bg_updates.py
@@ -425,7 +425,7 @@ class EventsBackgroundUpdatesStore(SQLBaseStore):
         """Background update to clean out extremities that should have been
         deleted previously.
 
-        Mainly used to deal with the aftermath of #5269.
+        Mainly used to deal with the aftermath of https://github.com/matrix-org/synapse/issues/5269.
         """
 
         # This works by first copying all existing forward extremities into the
@@ -558,7 +558,7 @@ class EventsBackgroundUpdatesStore(SQLBaseStore):
             )
 
             logger.info(
-                "Deleted %d forward extremities of %d checked, to clean up #5269",
+                "Deleted %d forward extremities of %d checked, to clean up matrix-org/synapse#5269",
                 deleted,
                 len(original_set),
             )
diff --git a/synapse/storage/databases/main/events_worker.py b/synapse/storage/databases/main/events_worker.py
index 4e63a16fa2..4125059061 100644
--- a/synapse/storage/databases/main/events_worker.py
+++ b/synapse/storage/databases/main/events_worker.py
@@ -1312,7 +1312,8 @@ class EventsWorkerStore(SQLBaseStore):
             room_version: Optional[RoomVersion]
             if not room_version_id:
                 # this should only happen for out-of-band membership events which
-                # arrived before #6983 landed. For all other events, we should have
+                # arrived before https://github.com/matrix-org/synapse/issues/6983
+                # landed. For all other events, we should have
                 # an entry in the 'rooms' table.
                 #
                 # However, the 'out_of_band_membership' flag is unreliable for older
@@ -1323,7 +1324,8 @@ class EventsWorkerStore(SQLBaseStore):
                         "Room %s for event %s is unknown" % (d["room_id"], event_id)
                     )
 
-                # so, assuming this is an out-of-band-invite that arrived before #6983
+                # so, assuming this is an out-of-band-invite that arrived before
+                # https://github.com/matrix-org/synapse/issues/6983
                 # landed, we know that the room version must be v5 or earlier (because
                 # v6 hadn't been invented at that point, so invites from such rooms
                 # would have been rejected.)
diff --git a/synapse/storage/databases/main/monthly_active_users.py b/synapse/storage/databases/main/monthly_active_users.py
index 4b1061e6d7..2911e53310 100644
--- a/synapse/storage/databases/main/monthly_active_users.py
+++ b/synapse/storage/databases/main/monthly_active_users.py
@@ -317,7 +317,7 @@ class MonthlyActiveUsersWorkerStore(RegistrationWorkerStore):
             if user_id:
                 is_support = self.is_support_user_txn(txn, user_id)
                 if not is_support:
-                    # We do this manually here to avoid hitting #6791
+                    # We do this manually here to avoid hitting https://github.com/matrix-org/synapse/issues/6791
                     self.db_pool.simple_upsert_txn(
                         txn,
                         table="monthly_active_users",
diff --git a/synapse/storage/databases/main/purge_events.py b/synapse/storage/databases/main/purge_events.py
index c3b3e2baaf..1a5b5731bb 100644
--- a/synapse/storage/databases/main/purge_events.py
+++ b/synapse/storage/databases/main/purge_events.py
@@ -494,7 +494,7 @@ class PurgeEventsStore(StateGroupWorkerStore, CacheInvalidationWorkerStore):
         #  - room_tags_revisions
         #       The problem with these is that they are largeish and there is no room_id
         #       index on them. In any case we should be clearing out 'stream' tables
-        #       periodically anyway (#5888)
+        #       periodically anyway (https://github.com/matrix-org/synapse/issues/5888)
 
         self._invalidate_caches_for_room_and_stream(txn, room_id)
 
diff --git a/synapse/storage/engines/postgres.py b/synapse/storage/engines/postgres.py
index 6309363217..ec4c4041b7 100644
--- a/synapse/storage/engines/postgres.py
+++ b/synapse/storage/engines/postgres.py
@@ -38,7 +38,8 @@ class PostgresEngine(
         super().__init__(psycopg2, database_config)
         psycopg2.extensions.register_type(psycopg2.extensions.UNICODE)
 
-        # Disables passing `bytes` to txn.execute, c.f. #6186. If you do
+        # Disables passing `bytes` to txn.execute, c.f.
+        # https://github.com/matrix-org/synapse/issues/6186. If you do
         # actually want to use bytes than wrap it in `bytearray`.
         def _disable_bytes_adapter(_: bytes) -> NoReturn:
             raise Exception("Passing bytes to DB is disabled.")
diff --git a/synapse/storage/schema/__init__.py b/synapse/storage/schema/__init__.py
index 158b528dce..03e5a0f55d 100644
--- a/synapse/storage/schema/__init__.py
+++ b/synapse/storage/schema/__init__.py
@@ -109,7 +109,8 @@ Changes in SCHEMA_VERSION = 78
 
 Changes in SCHEMA_VERSION = 79
     - Add tables to handle in DB read-write locks.
-    - Add some mitigations for a painful race between foreground and background updates, cf #15677.
+    - Add some mitigations for a painful race between foreground and background updates, cf
+      https://github.com/matrix-org/synapse/issues/15677.
 
 Changes in SCHEMA_VERSION = 80
     - The event_txn_id_device_id is always written to for new events.
diff --git a/synapse/storage/schema/main/delta/54/delete_forward_extremities.sql b/synapse/storage/schema/main/delta/54/delete_forward_extremities.sql
index b062ec840c..f713e42aa0 100644
--- a/synapse/storage/schema/main/delta/54/delete_forward_extremities.sql
+++ b/synapse/storage/schema/main/delta/54/delete_forward_extremities.sql
@@ -14,7 +14,7 @@
  */
 
 -- Start a background job to cleanup extremities that were incorrectly added
--- by bug #5269.
+-- by bug https://github.com/matrix-org/synapse/issues/5269.
 INSERT INTO background_updates (update_name, progress_json) VALUES
   ('delete_soft_failed_extremities', '{}');
 
diff --git a/synapse/storage/schema/main/delta/56/remove_tombstoned_rooms_from_directory.sql b/synapse/storage/schema/main/delta/56/remove_tombstoned_rooms_from_directory.sql
index aeb17813d3..246c3359f7 100644
--- a/synapse/storage/schema/main/delta/56/remove_tombstoned_rooms_from_directory.sql
+++ b/synapse/storage/schema/main/delta/56/remove_tombstoned_rooms_from_directory.sql
@@ -13,6 +13,7 @@
  * limitations under the License.
  */
 
--- Now that #6232 is a thing, we can remove old rooms from the directory.
+-- Now that https://github.com/matrix-org/synapse/pull/6232 is a thing, we can
+-- remove old rooms from the directory.
 INSERT INTO background_updates (update_name, progress_json) VALUES
   ('remove_tombstoned_rooms_from_directory', '{}');
diff --git a/synapse/storage/schema/main/delta/70/01clean_table_purged_rooms.sql b/synapse/storage/schema/main/delta/70/01clean_table_purged_rooms.sql
index aed79635b2..31a61defa7 100644
--- a/synapse/storage/schema/main/delta/70/01clean_table_purged_rooms.sql
+++ b/synapse/storage/schema/main/delta/70/01clean_table_purged_rooms.sql
@@ -13,7 +13,8 @@
  * limitations under the License.
  */
 
--- Clean up left over rows from bug #11833, which was fixed in #12770.
+-- Clean up left over rows from bug https://github.com/matrix-org/synapse/issues/11833,
+-- which was fixed in https://github.com/matrix-org/synapse/pull/12770.
 DELETE FROM federation_inbound_events_staging WHERE room_id not in (
     SELECT room_id FROM rooms
 );
diff --git a/synapse/util/check_dependencies.py b/synapse/util/check_dependencies.py
index f7cead9e12..6f008734a0 100644
--- a/synapse/util/check_dependencies.py
+++ b/synapse/util/check_dependencies.py
@@ -189,7 +189,8 @@ def check_requirements(extra: Optional[str] = None) -> None:
                 errors.append(_not_installed(requirement, extra))
         else:
             if dist.version is None:
-                # This shouldn't happen---it suggests a borked virtualenv. (See #12223)
+                # This shouldn't happen---it suggests a borked virtualenv. (See
+                # https://github.com/matrix-org/synapse/issues/12223)
                 # Try to give a vaguely helpful error message anyway.
                 # Type-ignore: the annotations don't reflect reality: see
                 #     https://github.com/python/typeshed/issues/7513
diff --git a/sytest-blacklist b/sytest-blacklist
index d5fa36cec7..9ec0cecfd4 100644
--- a/sytest-blacklist
+++ b/sytest-blacklist
@@ -29,5 +29,5 @@ We can't peek into rooms with joined history_visibility
 Local users can peek by room alias
 Peeked rooms only turn up in the sync for the device who peeked them
 
-# Validation needs to be added to Synapse: #10554
+# Validation needs to be added to Synapse: https://github.com/matrix-org/synapse/issues/10554
 Rejects invalid device keys
diff --git a/tests/federation/test_federation_sender.py b/tests/federation/test_federation_sender.py
index caf04b54cb..2c970fc827 100644
--- a/tests/federation/test_federation_sender.py
+++ b/tests/federation/test_federation_sender.py
@@ -478,7 +478,7 @@ class FederationSenderDevicesTestCases(HomeserverTestCase):
         # expect two edus, in one or two transactions. We don't know what order the
         # devices will be updated.
         self.assertEqual(len(self.edus), 2)
-        stream_id = None  # FIXME: there is a discontinuity in the stream IDs: see #7142
+        stream_id = None  # FIXME: there is a discontinuity in the stream IDs: see https://github.com/matrix-org/synapse/issues/7142
         for edu in self.edus:
             self.assertEqual(edu["edu_type"], EduTypes.DEVICE_LIST_UPDATE)
             c = edu["content"]
diff --git a/tests/handlers/test_federation.py b/tests/handlers/test_federation.py
index 4fc0742413..a035232905 100644
--- a/tests/handlers/test_federation.py
+++ b/tests/handlers/test_federation.py
@@ -112,7 +112,7 @@ class FederationTestCase(unittest.FederatingHomeserverTestCase):
         """
         Check that we store the state group correctly for rejected non-state events.
 
-        Regression test for #6289.
+        Regression test for https://github.com/matrix-org/synapse/issues/6289.
         """
         OTHER_SERVER = "otherserver"
         OTHER_USER = "@otheruser:" + OTHER_SERVER
@@ -165,7 +165,7 @@ class FederationTestCase(unittest.FederatingHomeserverTestCase):
         """
         Check that we store the state group correctly for rejected state events.
 
-        Regression test for #6289.
+        Regression test for https://github.com/matrix-org/synapse/issues/6289.
         """
         OTHER_SERVER = "otherserver"
         OTHER_USER = "@otheruser:" + OTHER_SERVER
@@ -222,7 +222,7 @@ class FederationTestCase(unittest.FederatingHomeserverTestCase):
         of backwards extremities(the magic number is more than 5),
         no errors are thrown.
 
-        Regression test, see #11027
+        Regression test, see https://github.com/matrix-org/synapse/pull/11027
         """
         # create the room
         user_id = self.register_user("kermit", "test")
diff --git a/tests/http/test_matrixfederationclient.py b/tests/http/test_matrixfederationclient.py
index bf1d287699..b7337d3926 100644
--- a/tests/http/test_matrixfederationclient.py
+++ b/tests/http/test_matrixfederationclient.py
@@ -368,7 +368,8 @@ class FederationClientTests(HomeserverTestCase):
         """
         If a connection is made to a client but the client rejects it due to
         requiring a trailing slash. We need to retry the request with a
-        trailing slash. Workaround for Synapse <= v0.99.3, explained in #3622.
+        trailing slash. Workaround for Synapse <= v0.99.3, explained in
+        https://github.com/matrix-org/synapse/issues/3622.
         """
         d = defer.ensureDeferred(
             self.cl.get_json("testserv:8008", "foo/bar", try_trailing_slash_on_400=True)
diff --git a/tests/push/test_bulk_push_rule_evaluator.py b/tests/push/test_bulk_push_rule_evaluator.py
index 7c23b77e0a..907ee1488c 100644
--- a/tests/push/test_bulk_push_rule_evaluator.py
+++ b/tests/push/test_bulk_push_rule_evaluator.py
@@ -92,7 +92,7 @@ class TestBulkPushRuleEvaluator(HomeserverTestCase):
         - the bad power level value for "room", before JSON serisalistion
         - whether Bob should expect the message to be highlighted
 
-        Reproduces #14060.
+        Reproduces https://github.com/matrix-org/synapse/issues/14060.
 
         A lack of validation: the gift that keeps on giving.
         """
diff --git a/tests/replication/tcp/streams/test_to_device.py b/tests/replication/tcp/streams/test_to_device.py
index ab379e8cf1..85adf84ece 100644
--- a/tests/replication/tcp/streams/test_to_device.py
+++ b/tests/replication/tcp/streams/test_to_device.py
@@ -62,7 +62,7 @@ class ToDeviceStreamTestCase(BaseStreamTestCase):
             )
 
         # add one more message, for user2 this time
-        # this message would be dropped before fixing #15335
+        # this message would be dropped before fixing https://github.com/matrix-org/synapse/issues/15335
         msg["content"] = {"device": {}}
         messages = {user2: {"device": msg}}
 
diff --git a/tests/rest/admin/test_user.py b/tests/rest/admin/test_user.py
index 42b065d883..492adb6160 100644
--- a/tests/rest/admin/test_user.py
+++ b/tests/rest/admin/test_user.py
@@ -1478,7 +1478,7 @@ class DeactivateAccountTestCase(unittest.HomeserverTestCase):
     def test_deactivate_user_erase_true_avatar_nonnull_but_empty(self) -> None:
         """Check we can erase a user whose avatar is the empty string.
 
-        Reproduces #12257.
+        Reproduces https://github.com/matrix-org/synapse/issues/12257.
         """
         # Patch `self.other_user` to have an empty string as their avatar.
         self.get_success(
diff --git a/tests/rest/client/test_events.py b/tests/rest/client/test_events.py
index 141e0f57a3..8bea860beb 100644
--- a/tests/rest/client/test_events.py
+++ b/tests/rest/client/test_events.py
@@ -64,7 +64,7 @@ class EventStreamPermissionsTestCase(unittest.HomeserverTestCase):
         # 403. However, since the v1 spec no longer exists and the v1
         # implementation is now part of the r0 implementation, the newer
         # behaviour is used instead to be consistent with the r0 spec.
-        # see issue #2602
+        # see issue https://github.com/matrix-org/synapse/issues/2602
         channel = self.make_request(
             "GET", "/events?access_token=%s" % ("invalid" + self.token,)
         )
diff --git a/tests/rest/client/test_profile.py b/tests/rest/client/test_profile.py
index ecae092b47..8f923fd40f 100644
--- a/tests/rest/client/test_profile.py
+++ b/tests/rest/client/test_profile.py
@@ -170,7 +170,8 @@ class ProfileTestCase(unittest.HomeserverTestCase):
         )
         self.assertEqual(channel.code, 200, channel.result)
         # FIXME: If a user has no displayname set, Synapse returns 200 and omits a
-        # displayname from the response. This contradicts the spec, see #13137.
+        # displayname from the response. This contradicts the spec, see
+        # https://github.com/matrix-org/synapse/issues/13137.
         return channel.json_body.get("displayname")
 
     def _get_avatar_url(self, name: Optional[str] = None) -> Optional[str]:
@@ -179,7 +180,8 @@ class ProfileTestCase(unittest.HomeserverTestCase):
         )
         self.assertEqual(channel.code, 200, channel.result)
         # FIXME: If a user has no avatar set, Synapse returns 200 and omits an
-        # avatar_url from the response. This contradicts the spec, see #13137.
+        # avatar_url from the response. This contradicts the spec, see
+        # https://github.com/matrix-org/synapse/issues/13137.
         return channel.json_body.get("avatar_url")
 
     @unittest.override_config({"max_avatar_size": 50})
diff --git a/tests/rest/client/test_rooms.py b/tests/rest/client/test_rooms.py
index aaa4f3bba0..bb24ed6aa7 100644
--- a/tests/rest/client/test_rooms.py
+++ b/tests/rest/client/test_rooms.py
@@ -888,7 +888,8 @@ class RoomsCreateTestCase(RoomBase):
     )
     def test_room_creation_ratelimiting(self) -> None:
         """
-        Regression test for #14312, where ratelimiting was made too strict.
+        Regression test for https://github.com/matrix-org/synapse/issues/14312,
+        where ratelimiting was made too strict.
         Clients should be able to create 10 rooms in a row
         without hitting rate limits, using default rate limit config.
         (We override rate limiting config back to its default value.)
diff --git a/tests/rest/client/test_sync.py b/tests/rest/client/test_sync.py
index d60665254e..07c81d7f76 100644
--- a/tests/rest/client/test_sync.py
+++ b/tests/rest/client/test_sync.py
@@ -642,7 +642,7 @@ class SyncCacheTestCase(unittest.HomeserverTestCase):
     def test_noop_sync_does_not_tightloop(self) -> None:
         """If the sync times out, we shouldn't cache the result
 
-        Essentially a regression test for #8518.
+        Essentially a regression test for https://github.com/matrix-org/synapse/issues/8518.
         """
         self.user_id = self.register_user("kermit", "monkey")
         self.tok = self.login("kermit", "monkey")
diff --git a/tests/storage/databases/main/test_lock.py b/tests/storage/databases/main/test_lock.py
index 35f77052a7..6c4d44c05c 100644
--- a/tests/storage/databases/main/test_lock.py
+++ b/tests/storage/databases/main/test_lock.py
@@ -66,9 +66,9 @@ class LockTestCase(unittest.HomeserverTestCase):
 
         # Run the tasks to completion.
         # To work around `Linearizer`s using a different reactor to sleep when
-        # contended (#12841), we call `runUntilCurrent` on
-        # `twisted.internet.reactor`, which is a different reactor to that used
-        # by the homeserver.
+        # contended (https://github.com/matrix-org/synapse/issues/12841), we call
+        # `runUntilCurrent` on `twisted.internet.reactor`, which is a different
+        # reactor to that used by the homeserver.
         assert isinstance(reactor, ReactorBase)
         self.get_success(task1)
         reactor.runUntilCurrent()
@@ -217,9 +217,9 @@ class ReadWriteLockTestCase(unittest.HomeserverTestCase):
 
         # Run the tasks to completion.
         # To work around `Linearizer`s using a different reactor to sleep when
-        # contended (#12841), we call `runUntilCurrent` on
-        # `twisted.internet.reactor`, which is a different reactor to that used
-        # by the homeserver.
+        # contended (https://github.com/matrix-org/synapse/issues/12841), we call
+        # `runUntilCurrent` on `twisted.internet.reactor`, which is a different
+        # reactor to that used by the homeserver.
         assert isinstance(reactor, ReactorBase)
         self.get_success(task1)
         reactor.runUntilCurrent()
@@ -269,9 +269,9 @@ class ReadWriteLockTestCase(unittest.HomeserverTestCase):
 
         # Run the tasks to completion.
         # To work around `Linearizer`s using a different reactor to sleep when
-        # contended (#12841), we call `runUntilCurrent` on
-        # `twisted.internet.reactor`, which is a different reactor to that used
-        # by the homeserver.
+        # contended (https://github.com/matrix-org/synapse/issues/12841), we call
+        # `runUntilCurrent` on `twisted.internet.reactor`, which is a different
+        # reactor to that used by the homeserver.
         assert isinstance(reactor, ReactorBase)
         self.get_success(task1)
         reactor.runUntilCurrent()
diff --git a/tests/storage/test_database.py b/tests/storage/test_database.py
index 92ddaa6f4c..d60176b1d4 100644
--- a/tests/storage/test_database.py
+++ b/tests/storage/test_database.py
@@ -214,7 +214,8 @@ class CallbacksTestCase(unittest.HomeserverTestCase):
         after_callback, exception_callback = self._run_interaction(_test_txn)
 
         # Calling both `after_callback`s when the first attempt failed is rather
-        # surprising (#12184). Let's document the behaviour in a test.
+        # surprising (https://github.com/matrix-org/synapse/issues/12184).
+        # Let's document the behaviour in a test.
         after_callback.assert_has_calls(
             [
                 call(123, 456, extra=789),
@@ -293,7 +294,7 @@ class PostgresReplicaIdentityTestCase(unittest.HomeserverTestCase):
     def test_all_tables_have_postgres_replica_identity(self) -> None:
         """
         Tests that all tables have a Postgres REPLICA IDENTITY.
-        (See #16224).
+        (See https://github.com/matrix-org/synapse/issues/16224).
 
         Tables with a PRIMARY KEY have an implied REPLICA IDENTITY and are fine.
         Other tables need them to be set with `ALTER TABLE`.
diff --git a/tests/storage/test_event_federation.py b/tests/storage/test_event_federation.py
index d3e20f44b2..66a027887d 100644
--- a/tests/storage/test_event_federation.py
+++ b/tests/storage/test_event_federation.py
@@ -1060,7 +1060,7 @@ class EventFederationWorkerStoreTestCase(tests.unittest.HomeserverTestCase):
         self,
     ) -> None:
         """
-        A test that reproduces #13929 (Postgres only).
+        A test that reproduces https://github.com/matrix-org/synapse/issues/13929 (Postgres only).
 
         Test to make sure we can still get backfill points after many failed pull
         attempts that cause us to backoff to the limit. Even if the backoff formula
diff --git a/tests/storage/test_room_search.py b/tests/storage/test_room_search.py
index 52ffa91c81..e3dc3623cb 100644
--- a/tests/storage/test_room_search.py
+++ b/tests/storage/test_room_search.py
@@ -93,7 +93,7 @@ class EventSearchInsertionTest(HomeserverTestCase):
         both strings and integers. When using Postgres, integers are automatically
         converted to strings.
 
-        Regression test for #11918.
+        Regression test for https://github.com/matrix-org/synapse/issues/11918.
         """
         store = self.hs.get_datastores().main
 
diff --git a/tests/util/test_check_dependencies.py b/tests/util/test_check_dependencies.py
index aa20fe6780..c1392d8bfc 100644
--- a/tests/util/test_check_dependencies.py
+++ b/tests/util/test_check_dependencies.py
@@ -89,7 +89,8 @@ class TestDependencyChecker(TestCase):
     def test_version_reported_as_none(self) -> None:
         """Complain if importlib.metadata.version() returns None.
 
-        This shouldn't normally happen, but it was seen in the wild (#12223).
+        This shouldn't normally happen, but it was seen in the wild
+        (https://github.com/matrix-org/synapse/issues/12223).
         """
         with patch(
             "synapse.util.check_dependencies.metadata.requires",
@@ -148,7 +149,7 @@ class TestDependencyChecker(TestCase):
         """
         Tests that release candidates count as far as satisfying a dependency
         is concerned.
-        (Regression test, see #12176.)
+        (Regression test, see https://github.com/matrix-org/synapse/issues/12176.)
         """
         with patch(
             "synapse.util.check_dependencies.metadata.requires",
@@ -162,7 +163,10 @@ class TestDependencyChecker(TestCase):
                 check_requirements()
 
     def test_setuptools_rust_ignored(self) -> None:
-        """Test a workaround for a `poetry build` problem. Reproduces #13926."""
+        """
+        Test a workaround for a `poetry build` problem. Reproduces
+        https://github.com/matrix-org/synapse/issues/13926.
+        """
         with patch(
             "synapse.util.check_dependencies.metadata.requires",
             return_value=["setuptools_rust >= 1.3"],