diff --git a/changelog.d/19090.bugfix b/changelog.d/19090.bugfix
new file mode 100644
index 00000000000..077dafcbf89
--- /dev/null
+++ b/changelog.d/19090.bugfix
@@ -0,0 +1 @@
+Fix lost logcontext warnings from timeouts in sync and requests made by Synapse itself.
diff --git a/synapse/logging/context.py b/synapse/logging/context.py
index 6a4425ff1de..45c83f0d61d 100644
--- a/synapse/logging/context.py
+++ b/synapse/logging/context.py
@@ -896,7 +896,7 @@ def run_in_background(
         # If the function messes with logcontexts, we can assume it follows the Synapse
         # logcontext rules (Rules for functions returning awaitables: "If the awaitable
         # is already complete, the function returns with the same logcontext it started
-        # with."). If it function doesn't touch logcontexts at all, we can also assume
+        # with."). If the function doesn't touch logcontexts at all, we can also assume
         # the logcontext is unchanged.
         #
         # Either way, the function should have maintained the calling logcontext, so we
@@ -905,11 +905,21 @@ def run_in_background(
         # to reset the logcontext to the sentinel logcontext as that would run
         # immediately (remember our goal is to maintain the calling logcontext when we
         # return).
-        logcontext_debug_logger.debug(
-            "run_in_background(%s): deferred already completed and the function should have maintained the logcontext %s",
-            instance_id,
-            calling_context,
-        )
+        if current_context() != calling_context:
+            logcontext_error(
+                "run_in_background(%s): deferred already completed but the function did not maintain the calling logcontext %s (found %s)"
+                % (
+                    instance_id,
+                    calling_context,
+                    current_context(),
+                )
+            )
+        else:
+            logcontext_debug_logger.debug(
+                "run_in_background(%s): deferred already completed and the function should have maintained the calling logcontext %s",
+                instance_id,
+                calling_context,
+            )
         return d
 
     # Since the function we called may follow the Synapse logcontext rules (Rules for
diff --git a/synapse/util/async_helpers.py b/synapse/util/async_helpers.py
index c568b377d24..99e899d1ef9 100644
--- a/synapse/util/async_helpers.py
+++ b/synapse/util/async_helpers.py
@@ -808,7 +808,8 @@ def time_it_out() -> None:
         timed_out[0] = True
 
         try:
-            deferred.cancel()
+            with PreserveLoggingContext():
+                deferred.cancel()
         except Exception:  # if we throw any exception it'll break time outs
             logger.exception("Canceller failed during timeout")
 
diff --git a/synapse/util/clock.py b/synapse/util/clock.py
index 6557582629e..5b59cef60a2 100644
--- a/synapse/util/clock.py
+++ b/synapse/util/clock.py
@@ -266,7 +266,7 @@ def wrapped_callback(*args: Any, **kwargs: Any) -> None:
                 # We use `PreserveLoggingContext` to prevent our new `call_later`
                 # logcontext from finishing as soon as we exit this function, in case `f`
                 # returns an awaitable/deferred which would continue running and may try to
-                # restore the `loop_call` context when it's done (because it's trying to
+                # restore the `call_later` context when it's done (because it's trying to
                 # adhere to the Synapse logcontext rules.)
                 #
                 # This also ensures that we return to the `sentinel` context when we exit
diff --git a/tests/unittest.py b/tests/unittest.py
index 1007f404561..049a92caaaf 100644
--- a/tests/unittest.py
+++ b/tests/unittest.py
@@ -341,6 +341,9 @@ def logcontext_clean(target: TV) -> TV:
     """
 
     def logcontext_error(msg: str) -> NoReturn:
+        # Log so we can still see it in the logs like normal
+        logger.warning(msg)
+        # But also fail the test
         raise AssertionError("logcontext error: %s" % (msg))
 
     patcher = patch("synapse.logging.context.logcontext_error", new=logcontext_error)
diff --git a/tests/util/test_async_helpers.py b/tests/util/test_async_helpers.py
index a02a2f0cef3..8fbee12fb90 100644
--- a/tests/util/test_async_helpers.py
+++ b/tests/util/test_async_helpers.py
@@ -45,7 +45,7 @@
 )
 
 from tests.server import get_clock
-from tests.unittest import TestCase
+from tests.unittest import TestCase, logcontext_clean
 
 logger = logging.getLogger(__name__)
 
@@ -198,7 +198,12 @@ def canceller(_d: Deferred) -> None:
 
         self.failureResultOf(timing_out_d, defer.TimeoutError)
 
-    async def test_logcontext_is_preserved_on_cancellation(self) -> None:
+    @logcontext_clean
+    async def test_logcontext_is_preserved_on_timeout_cancellation(self) -> None:
+        """
+        Test that the logcontext is preserved when we timeout and the deferred is
+        cancelled.
+        """
         # Sanity check that we start in the sentinel context
         self.assertEqual(current_context(), SENTINEL_CONTEXT)
 
@@ -270,6 +275,65 @@ def mark_was_cancelled(res: Failure) -> None:
         # Back to the sentinel context
         self.assertEqual(current_context(), SENTINEL_CONTEXT)
 
+    @logcontext_clean
+    async def test_logcontext_is_not_lost_when_awaiting_on_timeout_cancellation(
+        self,
+    ) -> None:
+        """
+        Test that the logcontext isn't lost when we `await make_deferred_yieldable(...)`
+        the deferred to complete/timeout and it times out.
+        """
+
+        # Sanity check that we start in the sentinel context
+        self.assertEqual(current_context(), SENTINEL_CONTEXT)
+
+        # Create a deferred which we will never complete
+        incomplete_d: Deferred = Deferred()
+
+        async def competing_task() -> None:
+            with LoggingContext(
+                name="competing", server_name="test_server"
+            ) as context_competing:
+                timing_out_d = timeout_deferred(
+                    deferred=incomplete_d,
+                    timeout=1.0,
+                    clock=self.clock,
+                )
+                self.assertNoResult(timing_out_d)
+                # We should still be in the logcontext we started in
+                self.assertIs(current_context(), context_competing)
+
+                # Mimic the normal use case to wait for the work to complete or timeout.
+                #
+                # In this specific test, we expect the deferred to timeout and raise an
+                # exception at this point.
+                await make_deferred_yieldable(timing_out_d)
+
+                self.fail(
+                    "We should not make it to this point as the `timing_out_d` should have been cancelled"
+                )
+
+        d = defer.ensureDeferred(competing_task())
+
+        # Still in the sentinel context
+        self.assertEqual(current_context(), SENTINEL_CONTEXT)
+
+        # Pump until we trigger the timeout
+        self.reactor.pump(
+            # We only need to pump `1.0` (seconds) as we set
+            # `timeout_deferred(timeout=1.0)` above
+            (1.0,)
+        )
+
+        # Still in the sentinel context
+        self.assertEqual(current_context(), SENTINEL_CONTEXT)
+
+        # We expect a failure due to the timeout
+        self.failureResultOf(d, defer.TimeoutError)
+
+        # Back to the sentinel context at the end of the day
+        self.assertEqual(current_context(), SENTINEL_CONTEXT)
+
 
 class _TestException(Exception):  #
     pass