diff --git a/changelog.d/7786.misc b/changelog.d/7786.misc
new file mode 100644
index 0000000000..27af2681dc
--- /dev/null
+++ b/changelog.d/7786.misc
@@ -0,0 +1 @@
+Update linting scripts and codebase to be compatible with `isort` v5.
diff --git a/scripts-dev/check_signature.py b/scripts-dev/check_signature.py
index ecda103cf7..6755bc5282 100644
--- a/scripts-dev/check_signature.py
+++ b/scripts-dev/check_signature.py
@@ -2,9 +2,9 @@ import argparse
 import json
 import logging
 import sys
-import urllib2
 
 import dns.resolver
+import urllib2
 from signedjson.key import decode_verify_key_bytes, write_signing_keys
 from signedjson.sign import verify_signed_json
 from unpaddedbase64 import decode_base64
diff --git a/scripts-dev/lint.sh b/scripts-dev/lint.sh
index 6f1ba22931..66b0568858 100755
--- a/scripts-dev/lint.sh
+++ b/scripts-dev/lint.sh
@@ -15,7 +15,7 @@ else
 fi
 
 echo "Linting these locations: $files"
-isort -y -rc $files
+isort $files
 python3 -m black $files
 ./scripts-dev/config-lint.sh
 flake8 $files
diff --git a/setup.cfg b/setup.cfg
index f2bca272e1..a32278ea8a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,7 +26,6 @@ ignore=W503,W504,E203,E731,E501
 
 [isort]
 line_length = 88
-not_skip = __init__.py
 sections=FUTURE,STDLIB,COMPAT,THIRDPARTY,TWISTED,FIRSTPARTY,TESTS,LOCALFOLDER
 default_section=THIRDPARTY
 known_first_party = synapse
diff --git a/synapse/api/auth.py b/synapse/api/auth.py
index 06ba6604f3..cb22508f4d 100644
--- a/synapse/api/auth.py
+++ b/synapse/api/auth.py
@@ -12,7 +12,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import logging
 from typing import Optional
 
@@ -22,7 +21,6 @@ from netaddr import IPAddress
 from twisted.internet import defer
 from twisted.web.server import Request
 
-import synapse.logging.opentracing as opentracing
 import synapse.types
 from synapse import event_auth
 from synapse.api.auth_blocking import AuthBlocking
@@ -35,6 +33,7 @@ from synapse.api.errors import (
 )
 from synapse.api.room_versions import KNOWN_ROOM_VERSIONS
 from synapse.events import EventBase
+from synapse.logging import opentracing as opentracing
 from synapse.types import StateMap, UserID
 from synapse.util.caches import register_cache
 from synapse.util.caches.lrucache import LruCache
diff --git a/synapse/config/__main__.py b/synapse/config/__main__.py
index fca35b008c..65043d5b5b 100644
--- a/synapse/config/__main__.py
+++ b/synapse/config/__main__.py
@@ -16,6 +16,7 @@ from synapse.config._base import ConfigError
 
 if __name__ == "__main__":
     import sys
+
     from synapse.config.homeserver import HomeServerConfig
 
     action = sys.argv[1]
diff --git a/synapse/config/emailconfig.py b/synapse/config/emailconfig.py
index ca61214454..df08bcd1bc 100644
--- a/synapse/config/emailconfig.py
+++ b/synapse/config/emailconfig.py
@@ -14,7 +14,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 from __future__ import print_function
 
 # This file can't be called email.py because if it is, we cannot:
@@ -145,8 +144,8 @@ class EmailConfig(Config):
             or self.threepid_behaviour_email == ThreepidBehaviour.LOCAL
         ):
             # make sure we can import the required deps
-            import jinja2
             import bleach
+            import jinja2
 
             # prevent unused warnings
             jinja2
diff --git a/synapse/handlers/auth.py b/synapse/handlers/auth.py
index d713a06bf9..a162392e4c 100644
--- a/synapse/handlers/auth.py
+++ b/synapse/handlers/auth.py
@@ -13,7 +13,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import logging
 import time
 import unicodedata
@@ -24,7 +23,6 @@ import attr
 import bcrypt  # type: ignore[import]
 import pymacaroons
 
-import synapse.util.stringutils as stringutils
 from synapse.api.constants import LoginType
 from synapse.api.errors import (
     AuthError,
@@ -45,6 +43,7 @@ from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.module_api import ModuleApi
 from synapse.push.mailer import load_jinja2_templates
 from synapse.types import Requester, UserID
+from synapse.util import stringutils as stringutils
 from synapse.util.threepids import canonicalise_email
 
 from ._base import BaseHandler
diff --git a/synapse/handlers/cas_handler.py b/synapse/handlers/cas_handler.py
index 76f213723a..d79ffefdb5 100644
--- a/synapse/handlers/cas_handler.py
+++ b/synapse/handlers/cas_handler.py
@@ -12,11 +12,10 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import logging
 import urllib
-import xml.etree.ElementTree as ET
 from typing import Dict, Optional, Tuple
+from xml.etree import ElementTree as ET
 
 from twisted.web.client import PartialDownloadError
 
diff --git a/synapse/logging/opentracing.py b/synapse/logging/opentracing.py
index 1676771ef0..c6c0e623c1 100644
--- a/synapse/logging/opentracing.py
+++ b/synapse/logging/opentracing.py
@@ -164,7 +164,6 @@ Gotchas
   than one caller? Will all of those calling functions have be in a context
   with an active span?
 """
-
 import contextlib
 import inspect
 import logging
@@ -180,8 +179,8 @@ from twisted.internet import defer
 from synapse.config import ConfigError
 
 if TYPE_CHECKING:
-    from synapse.server import HomeServer
     from synapse.http.site import SynapseRequest
+    from synapse.server import HomeServer
 
 # Helper class
 
@@ -227,6 +226,7 @@ except ImportError:
     tags = _DummyTagNames
 try:
     from jaeger_client import Config as JaegerConfig
+
     from synapse.logging.scopecontextmanager import LogContextScopeManager
 except ImportError:
     JaegerConfig = None  # type: ignore
diff --git a/synapse/replication/tcp/client.py b/synapse/replication/tcp/client.py
index df29732f51..4985e40b1f 100644
--- a/synapse/replication/tcp/client.py
+++ b/synapse/replication/tcp/client.py
@@ -33,8 +33,8 @@ from synapse.util.async_helpers import timeout_deferred
 from synapse.util.metrics import Measure
 
 if TYPE_CHECKING:
-    from synapse.server import HomeServer
     from synapse.replication.tcp.handler import ReplicationCommandHandler
+    from synapse.server import HomeServer
 
 logger = logging.getLogger(__name__)
 
diff --git a/synapse/replication/tcp/handler.py b/synapse/replication/tcp/handler.py
index e6a2e2598b..55b3b79008 100644
--- a/synapse/replication/tcp/handler.py
+++ b/synapse/replication/tcp/handler.py
@@ -13,7 +13,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import logging
 from typing import Any, Dict, Iterable, Iterator, List, Optional, Set, Tuple, TypeVar
 
@@ -149,10 +148,11 @@ class ReplicationCommandHandler:
         using TCP.
         """
         if hs.config.redis.redis_enabled:
+            import txredisapi
+
             from synapse.replication.tcp.redis import (
                 RedisDirectTcpReplicationClientFactory,
             )
-            import txredisapi
 
             logger.info(
                 "Connecting to redis (host=%r port=%r)",
diff --git a/synapse/replication/tcp/streams/events.py b/synapse/replication/tcp/streams/events.py
index f370390331..bdddb62ad6 100644
--- a/synapse/replication/tcp/streams/events.py
+++ b/synapse/replication/tcp/streams/events.py
@@ -13,7 +13,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import heapq
 from collections import Iterable
 from typing import List, Tuple, Type
@@ -22,7 +21,6 @@ import attr
 
 from ._base import Stream, StreamUpdateResult, Token, current_token_without_instance
 
-
 """Handling of the 'events' replication stream
 
 This stream contains rows of various types. Each row therefore contains a 'type'
diff --git a/synapse/rest/media/v1/thumbnailer.py b/synapse/rest/media/v1/thumbnailer.py
index c234ea7421..7126997134 100644
--- a/synapse/rest/media/v1/thumbnailer.py
+++ b/synapse/rest/media/v1/thumbnailer.py
@@ -12,11 +12,10 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import logging
 from io import BytesIO
 
-import PIL.Image as Image
+from PIL import Image as Image
 
 logger = logging.getLogger(__name__)
 
diff --git a/synapse/secrets.py b/synapse/secrets.py
index 0b327a0f82..5f43f81eb0 100644
--- a/synapse/secrets.py
+++ b/synapse/secrets.py
@@ -19,7 +19,6 @@ Injectable secrets module for Synapse.
 See https://docs.python.org/3/library/secrets.html#module-secrets for the API
 used in Python 3.6, and the API emulated in Python 2.7.
 """
-
 import sys
 
 # secrets is available since python 3.6
@@ -31,8 +30,8 @@ if sys.version_info[0:2] >= (3, 6):
 
 
 else:
-    import os
     import binascii
+    import os
 
     class Secrets(object):
         def token_bytes(self, nbytes=32):
diff --git a/synapse/storage/data_stores/main/events.py b/synapse/storage/data_stores/main/events.py
index cfd24d2f06..b7bf3fbd9d 100644
--- a/synapse/storage/data_stores/main/events.py
+++ b/synapse/storage/data_stores/main/events.py
@@ -14,7 +14,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import itertools
 import logging
 from collections import OrderedDict, namedtuple
@@ -48,8 +47,8 @@ from synapse.util.frozenutils import frozendict_json_encoder
 from synapse.util.iterutils import batch_iter
 
 if TYPE_CHECKING:
-    from synapse.storage.data_stores.main import DataStore
     from synapse.server import HomeServer
+    from synapse.storage.data_stores.main import DataStore
 
 
 logger = logging.getLogger(__name__)
diff --git a/synapse/storage/data_stores/main/ui_auth.py b/synapse/storage/data_stores/main/ui_auth.py
index ec2f38c373..4c044b1a15 100644
--- a/synapse/storage/data_stores/main/ui_auth.py
+++ b/synapse/storage/data_stores/main/ui_auth.py
@@ -17,10 +17,10 @@ from typing import Any, Dict, Optional, Union
 
 import attr
 
-import synapse.util.stringutils as stringutils
 from synapse.api.errors import StoreError
 from synapse.storage._base import SQLBaseStore
 from synapse.types import JsonDict
+from synapse.util import stringutils as stringutils
 
 
 @attr.s
diff --git a/synapse/storage/types.py b/synapse/storage/types.py
index daff81c5ee..2d2b560e74 100644
--- a/synapse/storage/types.py
+++ b/synapse/storage/types.py
@@ -12,12 +12,10 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 from typing import Any, Iterable, Iterator, List, Tuple
 
 from typing_extensions import Protocol
 
-
 """
 Some very basic protocol definitions for the DB-API2 classes specified in PEP-249
 """
diff --git a/synapse/types.py b/synapse/types.py
index acf60baddc..238b938064 100644
--- a/synapse/types.py
+++ b/synapse/types.py
@@ -29,7 +29,7 @@ from synapse.api.errors import Codes, SynapseError
 if sys.version_info[:3] >= (3, 6, 0):
     from typing import Collection
 else:
-    from typing import Sized, Iterable, Container
+    from typing import Container, Iterable, Sized
 
     T_co = TypeVar("T_co", covariant=True)
 
diff --git a/tests/handlers/test_e2e_keys.py b/tests/handlers/test_e2e_keys.py
index 6c1dc72bd1..1acf287ca4 100644
--- a/tests/handlers/test_e2e_keys.py
+++ b/tests/handlers/test_e2e_keys.py
@@ -14,11 +14,9 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import mock
 
-import signedjson.key as key
-import signedjson.sign as sign
+from signedjson import key as key, sign as sign
 
 from twisted.internet import defer
 
diff --git a/tests/rest/media/v1/test_media_storage.py b/tests/rest/media/v1/test_media_storage.py
index 2ed9312d56..66fa5978b2 100644
--- a/tests/rest/media/v1/test_media_storage.py
+++ b/tests/rest/media/v1/test_media_storage.py
@@ -12,8 +12,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
 import os
 import shutil
 import tempfile
@@ -25,8 +23,8 @@ from urllib import parse
 from mock import Mock
 
 import attr
-import PIL.Image as Image
 from parameterized import parameterized_class
+from PIL import Image as Image
 
 from twisted.internet.defer import Deferred
 
diff --git a/tests/test_utils/event_injection.py b/tests/test_utils/event_injection.py
index 431e9f8e5e..43297b530c 100644
--- a/tests/test_utils/event_injection.py
+++ b/tests/test_utils/event_injection.py
@@ -13,7 +13,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 from typing import Optional, Tuple
 
 import synapse.server
@@ -25,7 +24,6 @@ from synapse.types import Collection
 
 from tests.test_utils import get_awaitable_result
 
-
 """
 Utility functions for poking events into the storage of the server under test.
 """
diff --git a/tox.ini b/tox.ini
index ab6557f15e..1c042cb227 100644
--- a/tox.ini
+++ b/tox.ini
@@ -131,8 +131,8 @@ commands =
 
 [testenv:check_isort]
 skip_install = True
-deps = isort
-commands = /bin/sh -c "isort -c -df -sp setup.cfg -rc synapse tests scripts-dev scripts"
+deps = isort==5.0.3
+commands = /bin/sh -c "isort -c --df --sp setup.cfg synapse tests scripts-dev scripts"
 
 [testenv:check-newsfragment]
 skip_install = True