diff --git a/changelog.d/13368.misc b/changelog.d/13368.misc
new file mode 100644
index 000000000000..4b433a510781
--- /dev/null
+++ b/changelog.d/13368.misc
@@ -0,0 +1 @@
+Instrument `/messages` for understandable traces in Jaeger.
diff --git a/synapse/api/auth.py b/synapse/api/auth.py
index 6e6eaf3805bd..c6f8733e6017 100644
--- a/synapse/api/auth.py
+++ b/synapse/api/auth.py
@@ -30,7 +30,12 @@
 from synapse.appservice import ApplicationService
 from synapse.http import get_request_user_agent
 from synapse.http.site import SynapseRequest
-from synapse.logging.opentracing import active_span, force_tracing, start_active_span
+from synapse.logging.opentracing import (
+    active_span,
+    force_tracing,
+    start_active_span,
+    trace,
+)
 from synapse.storage.databases.main.registration import TokenLookupResult
 from synapse.types import Requester, UserID, create_requester
 
@@ -563,6 +568,7 @@ def get_access_token_from_request(request: Request) -> str:
 
             return query_params[0].decode("ascii")
 
+    @trace
     async def check_user_in_room_or_world_readable(
         self, room_id: str, user_id: str, allow_departed_users: bool = False
     ) -> Tuple[str, Optional[str]]:
diff --git a/synapse/federation/federation_client.py b/synapse/federation/federation_client.py
index 842f5327c227..c1f96328b44a 100644
--- a/synapse/federation/federation_client.py
+++ b/synapse/federation/federation_client.py
@@ -61,6 +61,7 @@
 )
 from synapse.federation.transport.client import SendJoinResponse
 from synapse.http.types import QueryParams
+from synapse.logging.opentracing import trace
 from synapse.types import JsonDict, UserID, get_domain_from_id
 from synapse.util.async_helpers import concurrently_execute
 from synapse.util.caches.expiringcache import ExpiringCache
@@ -233,6 +234,7 @@ async def claim_client_keys(
             destination, content, timeout
         )
 
+    @trace
     async def backfill(
         self, dest: str, room_id: str, limit: int, extremities: Collection[str]
     ) -> Optional[List[EventBase]]:
diff --git a/synapse/handlers/federation.py b/synapse/handlers/federation.py
index 3b5eaf515624..59580ef93e55 100644
--- a/synapse/handlers/federation.py
+++ b/synapse/handlers/federation.py
@@ -59,6 +59,7 @@
 from synapse.federation.federation_client import InvalidResponseError
 from synapse.http.servlet import assert_params_in_dict
 from synapse.logging.context import nested_logging_context
+from synapse.logging.opentracing import trace
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.module_api import NOT_SPAM
 from synapse.replication.http.federation import (
@@ -180,6 +181,7 @@ def __init__(self, hs: "HomeServer"):
                 "resume_sync_partial_state_room", self._resume_sync_partial_state_room
             )
 
+    @trace
     async def maybe_backfill(
         self, room_id: str, current_depth: int, limit: int
     ) -> bool:
diff --git a/synapse/handlers/federation_event.py b/synapse/handlers/federation_event.py
index 16f20c8be7bc..4429319265db 100644
--- a/synapse/handlers/federation_event.py
+++ b/synapse/handlers/federation_event.py
@@ -59,6 +59,7 @@
 from synapse.events.snapshot import EventContext
 from synapse.federation.federation_client import InvalidResponseError
 from synapse.logging.context import nested_logging_context
+from synapse.logging.opentracing import trace
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.replication.http.devices import ReplicationUserDevicesResyncRestServlet
 from synapse.replication.http.federation import (
@@ -560,6 +561,7 @@ async def update_state_for_partial_state_event(
                 event.event_id
             )
 
+    @trace
     async def backfill(
         self, dest: str, room_id: str, limit: int, extremities: Collection[str]
     ) -> None:
@@ -604,6 +606,7 @@ async def backfill(
             backfilled=True,
         )
 
+    @trace
     async def _get_missing_events_for_pdu(
         self, origin: str, pdu: EventBase, prevs: Set[str], min_depth: int
     ) -> None:
@@ -704,6 +707,7 @@ async def _get_missing_events_for_pdu(
         logger.info("Got %d prev_events", len(missing_events))
         await self._process_pulled_events(origin, missing_events, backfilled=False)
 
+    @trace
     async def _process_pulled_events(
         self, origin: str, events: Iterable[EventBase], backfilled: bool
     ) -> None:
@@ -742,6 +746,7 @@ async def _process_pulled_events(
             with nested_logging_context(ev.event_id):
                 await self._process_pulled_event(origin, ev, backfilled=backfilled)
 
+    @trace
     async def _process_pulled_event(
         self, origin: str, event: EventBase, backfilled: bool
     ) -> None:
diff --git a/synapse/handlers/pagination.py b/synapse/handlers/pagination.py
index 6262a35822f3..e1e34e3b16ba 100644
--- a/synapse/handlers/pagination.py
+++ b/synapse/handlers/pagination.py
@@ -24,6 +24,7 @@
 from synapse.api.filtering import Filter
 from synapse.events.utils import SerializeEventConfig
 from synapse.handlers.room import ShutdownRoomResponse
+from synapse.logging.opentracing import trace
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage.state import StateFilter
 from synapse.streams.config import PaginationConfig
@@ -416,6 +417,7 @@ async def purge_room(self, room_id: str, force: bool = False) -> None:
 
             await self._storage_controllers.purge_events.purge_room(room_id)
 
+    @trace
     async def get_messages(
         self,
         requester: Requester,
diff --git a/synapse/handlers/relations.py b/synapse/handlers/relations.py
index 0b63cd218615..a02fc45e710d 100644
--- a/synapse/handlers/relations.py
+++ b/synapse/handlers/relations.py
@@ -19,6 +19,7 @@
 from synapse.api.constants import RelationTypes
 from synapse.api.errors import SynapseError
 from synapse.events import EventBase, relation_from_event
+from synapse.logging.opentracing import trace
 from synapse.storage.databases.main.relations import _RelatedEvent
 from synapse.types import JsonDict, Requester, StreamToken, UserID
 from synapse.visibility import filter_events_for_client
@@ -364,6 +365,7 @@ async def _get_threads_for_events(
 
         return results
 
+    @trace
     async def get_bundled_aggregations(
         self, events: Iterable[EventBase], user_id: str
     ) -> Dict[str, BundledAggregations]:
diff --git a/synapse/storage/controllers/state.py b/synapse/storage/controllers/state.py
index e08f956e6ef7..f584e6c92e2c 100644
--- a/synapse/storage/controllers/state.py
+++ b/synapse/storage/controllers/state.py
@@ -29,6 +29,7 @@
 
 from synapse.api.constants import EventTypes
 from synapse.events import EventBase
+from synapse.logging.opentracing import trace
 from synapse.storage.state import StateFilter
 from synapse.storage.util.partial_state_events_tracker import (
     PartialCurrentStateTracker,
@@ -175,6 +176,7 @@ def _get_state_groups_from_groups(
 
         return self.stores.state._get_state_groups_from_groups(groups, state_filter)
 
+    @trace
     async def get_state_for_events(
         self, event_ids: Collection[str], state_filter: Optional[StateFilter] = None
     ) -> Dict[str, StateMap[EventBase]]:
@@ -221,6 +223,7 @@ async def get_state_for_events(
 
         return {event: event_to_state[event] for event in event_ids}
 
+    @trace
     async def get_state_ids_for_events(
         self,
         event_ids: Collection[str],
@@ -283,6 +286,7 @@ async def get_state_for_event(
         )
         return state_map[event_id]
 
+    @trace
     async def get_state_ids_for_event(
         self, event_id: str, state_filter: Optional[StateFilter] = None
     ) -> StateMap[str]:
@@ -323,6 +327,7 @@ def get_state_for_groups(
             groups, state_filter or StateFilter.all()
         )
 
+    @trace
     async def get_state_group_for_events(
         self,
         event_ids: Collection[str],
diff --git a/synapse/storage/databases/main/stream.py b/synapse/storage/databases/main/stream.py
index 2590b52f7352..a347430aa7e3 100644
--- a/synapse/storage/databases/main/stream.py
+++ b/synapse/storage/databases/main/stream.py
@@ -58,6 +58,7 @@
 from synapse.api.filtering import Filter
 from synapse.events import EventBase
 from synapse.logging.context import make_deferred_yieldable, run_in_background
+from synapse.logging.opentracing import trace
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.database import (
     DatabasePool,
@@ -1346,6 +1347,7 @@ def _paginate_room_events_txn(
 
         return rows, next_token
 
+    @trace
     async def paginate_room_events(
         self,
         room_id: str,
diff --git a/synapse/streams/events.py b/synapse/streams/events.py
index 54e0b1a23b6f..bcd840bd88c1 100644
--- a/synapse/streams/events.py
+++ b/synapse/streams/events.py
@@ -21,6 +21,7 @@
 from synapse.handlers.receipts import ReceiptEventSource
 from synapse.handlers.room import RoomEventSource
 from synapse.handlers.typing import TypingNotificationEventSource
+from synapse.logging.opentracing import trace
 from synapse.streams import EventSource
 from synapse.types import StreamToken
 
@@ -69,6 +70,7 @@ def get_current_token(self) -> StreamToken:
         )
         return token
 
+    @trace
     async def get_current_token_for_pagination(self, room_id: str) -> StreamToken:
         """Get the current token for a given room to be used to paginate
         events.
diff --git a/synapse/visibility.py b/synapse/visibility.py
index 9abbaa5a6464..d947edde66dd 100644
--- a/synapse/visibility.py
+++ b/synapse/visibility.py
@@ -23,6 +23,7 @@
 from synapse.events import EventBase
 from synapse.events.snapshot import EventContext
 from synapse.events.utils import prune_event
+from synapse.logging.opentracing import trace
 from synapse.storage.controllers import StorageControllers
 from synapse.storage.databases.main import DataStore
 from synapse.storage.state import StateFilter
@@ -51,6 +52,7 @@
 _HISTORY_VIS_KEY: Final[Tuple[str, str]] = (EventTypes.RoomHistoryVisibility, "")
 
 
+@trace
 async def filter_events_for_client(
     storage: StorageControllers,
     user_id: str,