diff --git a/changelog.d/7786.misc b/changelog.d/7786.misc
new file mode 100644
index 0000000000000000000000000000000000000000..27af2681dc658b891b07de7f60a38d66a7c4b361
--- /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 ecda103cf7c4794db61badec7c7495ce374e09e6..6755bc528287d759970cc5fd908cb71f9cb60c5b 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 6f1ba22931962fb9fd256d6f88ae81fd860db058..66b0568858797947f98da65487fe3cb1095b14e6 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 f2bca272e17c42d13c13bbafc0b249375f8644f0..a32278ea8a08704a643b715054b94c6ad825ce69 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 06ba6604f3270ac055c8bc26e94783b2eb7181b4..cb22508f4d76b5ebb01b018d6eff3b269bc014b6 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 fca35b008c6ec063c0ebc557df9696a6fb0b45f6..65043d5b5b5f2b197c10ed250c8710a2a7adb87d 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 ca61214454f8cbb1de9352a20f800e204fd6a604..df08bcd1bcaf776cf5392e8283b79129c2c8f231 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 d713a06bf91853e9d666e0df032f2417d7994eaf..a162392e4cb3abb1452dd1b2171ce29383ba0333 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 76f213723a0d3f4ded759e8b383677e6b379d4a1..d79ffefdb56399bbbe1268d064e5f1b0fb2118bc 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 1676771ef0fb93bb5c12b607275eb1ed57823782..c6c0e623c16e85472e0b8c925a55aed1ede20aa2 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 df29732f51a106f8009da70fadffd25247b53834..4985e40b1ff434aebbafa04fa80b38663567fbb6 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 e6a2e2598b66a8f3cd13285827f29f3f7ed7be8b..55b3b790087634ff90adf5176c9cc514266fc0fb 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 f3703903314d5da173732ec997ce1e7fc82582ee..bdddb62ad634f88ae73bd56d4d94aab43e9749dd 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 c234ea74212fdd7934f18981387406e95fd6e716..7126997134d27efda1b75e7a04845c884dff8527 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 0b327a0f823363763fccfacd1df11dea588e1e35..5f43f81eb0fd1b1c61115fb399fb112eecd93b66 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 cfd24d2f061d59197363b6ef1154e2e6907114ed..b7bf3fbd9d368affef0a197ac9f7b69b17b6bc02 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 ec2f38c37357d53320e86a8a0ab937294cd93700..4c044b1a15491ed181b2754e0eb22a66cd5f971d 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 daff81c5ee23ee9e7c367f6f14a16c8e2f954a87..2d2b560e748e1c4cc255d2dc6eb929fd9a2991b4 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 acf60baddc6bd09afe920fd6a010fa62ab0ef837..238b9380644832d1643f70eda0541369efd3b24b 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 6c1dc72bd11166615a1cb63fa98b0168e3fa4f3a..1acf287ca4e882c9c5c8be9bce1bd8fe6174ff93 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 2ed9312d564dd1e5fd5a874710c933ebc1777cd4..66fa5978b2fd527086afbe60b33b93f478280334 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 431e9f8e5e3457315778affe9492e43f0e197c51..43297b530cbe6753067090523e8687ec4622e0e2 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 ab6557f15e71b74937b0efbc6a994bd652ef46b0..1c042cb2271e2f1ea0a4c8986e7f889ad63c1bac 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