diff --git a/docs/changelog/3869.bugfix.rst b/docs/changelog/3869.bugfix.rst
new file mode 100644
index 0000000000..e1d3cb1bca
--- /dev/null
+++ b/docs/changelog/3869.bugfix.rst
@@ -0,0 +1,2 @@
+Break deadlock in execution interrupt chain that caused ~18 flaky timeout failures across 9 tests on Windows/macOS CI -
+by :user:`gaborbernat`.
diff --git a/src/tox/session/cmd/run/common.py b/src/tox/session/cmd/run/common.py
index 84f4f9f440..311997c257 100644
--- a/src/tox/session/cmd/run/common.py
+++ b/src/tox/session/cmd/run/common.py
@@ -6,7 +6,8 @@
 import os
 import time
 from argparse import Action, ArgumentError, ArgumentParser, Namespace
-from concurrent.futures import CancelledError, Future, ThreadPoolExecutor, as_completed
+from concurrent.futures import FIRST_COMPLETED, CancelledError, Future, ThreadPoolExecutor
+from concurrent.futures import wait as wait_futures
 from fnmatch import fnmatchcase
 from pathlib import Path
 from signal import SIGINT, Handlers, signal
@@ -227,7 +228,8 @@ def execute(state: State, max_workers: int | None, has_spinner: bool, live: bool
         )
         thread.start()
         try:
-            thread.join()
+            while thread.is_alive():
+                thread.join(timeout=1)
         except KeyboardInterrupt:
             previous, has_previous = signal(SIGINT, Handlers.SIG_IGN), True
             spinner.print_report = False  # no need to print reports at this point, final report coming up
@@ -287,6 +289,18 @@ def update_spinner(self, result: ToxEnvRunResult, success: bool) -> None:  # noq
         done(result.name)
 
 
+def _next_completed(
+    future_to_env: dict[Future[ToxEnvRunResult], ToxEnv],
+    interrupt: Event,
+) -> Future[ToxEnvRunResult] | None:
+    while True:
+        done_futures, _ = wait_futures(list(future_to_env), timeout=1, return_when=FIRST_COMPLETED)
+        if done_futures:
+            return done_futures.pop()
+        if interrupt.is_set():
+            return None
+
+
 def _queue_and_wait(  # noqa: C901, PLR0913, PLR0915, PLR0912
     state: State,
     to_run_list: list[str],
@@ -337,32 +351,40 @@ def _run(tox_env: RunToxEnv) -> ToxEnvRunResult:
 
                     if not future_to_env:
                         result: ToxEnvRunResult | None = None
-                    else:  # if we have queued wait for completed
-                        future = next(as_completed(future_to_env))
-                        tox_env_done = future_to_env.pop(future)
-                        try:
-                            result = future.result()
-                        except CancelledError:
-                            tox_env_done.teardown()
-                            name = tox_env_done.conf.name
-                            result = ToxEnvRunResult(
-                                name=name,
-                                skipped=False,
-                                code=-3,
-                                outcomes=[],
-                                duration=MISS_DURATION,
-                            )
-                        results.append(result)
-                        completed.add(result.name)
-                        if (
-                            result.code != Outcome.OK
-                            and not result.ignore_outcome
-                            and (options.parsed.fail_fast or result.fail_fast)
-                        ):
-                            interrupt.set()
+                    else:
+                        completed_future = _next_completed(future_to_env, interrupt)
+                        if completed_future is None:
+                            for pending_future, pending_env in list(future_to_env.items()):
+                                if not pending_future.cancel() and not pending_future.done():
+                                    pending_env.interrupt()
+                            future_to_env.clear()
                             env_list = []
-                            for pending_future in list(future_to_env.keys()):
-                                pending_future.cancel()
+                            result = None
+                        else:
+                            tox_env_done = future_to_env.pop(completed_future)
+                            try:
+                                result = completed_future.result()
+                            except CancelledError:
+                                tox_env_done.teardown()
+                                name = tox_env_done.conf.name
+                                result = ToxEnvRunResult(
+                                    name=name,
+                                    skipped=False,
+                                    code=-3,
+                                    outcomes=[],
+                                    duration=MISS_DURATION,
+                                )
+                            results.append(result)
+                            completed.add(result.name)
+                            if (
+                                result.code != Outcome.OK
+                                and not result.ignore_outcome
+                                and (options.parsed.fail_fast or result.fail_fast)
+                            ):
+                                interrupt.set()
+                                env_list = []
+                                for pending_future in list(future_to_env.keys()):
+                                    pending_future.cancel()
 
                     if not interrupt.is_set() and not env_list:
                         env_list = next(envs_to_run_generator, [])