diff --git a/strix/telemetry/logging.py b/strix/telemetry/logging.py
index dad9255b..c8e4bce2 100644
--- a/strix/telemetry/logging.py
+++ b/strix/telemetry/logging.py
@@ -168,6 +168,17 @@ def attach_preflight_logging(*, debug: bool | None = None) -> None:
         logging.getLogger(name).setLevel(logging.WARNING)
 
 
+def remove_preflight_logging() -> None:
+    """Detach any preflight stderr handler from the tracked logger roots."""
+    for name in _TRACKED_ROOTS:
+        tracked = logging.getLogger(name)
+        for handler in list(tracked.handlers):
+            if getattr(handler, _PREFLIGHT_HANDLER_TAG, False):
+                tracked.removeHandler(handler)
+                with contextlib.suppress(Exception):
+                    handler.close()
+
+
 def setup_scan_logging(run_dir: Path, *, debug: bool | None = None) -> Callable[[], None]:
     """Attach scan-scoped handlers; return a teardown callable.
 
@@ -185,6 +196,7 @@ def setup_scan_logging(run_dir: Path, *, debug: bool | None = None) -> Callable[
         time. Safe to call from a ``finally`` block.
     """
     configure_dependency_logging()
+    remove_preflight_logging()
 
     debug = debug_logging_enabled(debug=debug)
 
diff --git a/tests/test_preflight_logging.py b/tests/test_preflight_logging.py
index caee9a84..d4f6ef48 100644
--- a/tests/test_preflight_logging.py
+++ b/tests/test_preflight_logging.py
@@ -11,20 +11,26 @@ from strix.interface.main import (
     _format_connection_error_detail,
 )
 from strix.telemetry import logging as tlog
-from strix.telemetry.logging import attach_preflight_logging, debug_logging_enabled
+from strix.telemetry.logging import (
+    attach_preflight_logging,
+    debug_logging_enabled,
+    remove_preflight_logging,
+    setup_scan_logging,
+)
 
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     import pytest
 
 
-def _remove_preflight_handlers() -> None:
-    for tracked_name in ("strix", "openai.agents"):
-        tracked = logging.getLogger(tracked_name)
-        for handler in list(tracked.handlers):
-            if getattr(handler, tlog._PREFLIGHT_HANDLER_TAG, False):
-                tracked.removeHandler(handler)
-                handler.close()
+def _preflight_handlers(name: str) -> list[logging.Handler]:
+    return [
+        handler
+        for handler in logging.getLogger(name).handlers
+        if getattr(handler, tlog._PREFLIGHT_HANDLER_TAG, False)
+    ]
 
 
 def test_exception_messages_walks_cause_chain_to_ssl_error() -> None:
@@ -77,4 +83,20 @@ def test_attach_preflight_logging_emits_debug_to_stderr(
         captured = capsys.readouterr()
         assert "LLM warm-up failed" in captured.err
     finally:
-        _remove_preflight_handlers()
+        remove_preflight_logging()
+
+
+def test_setup_scan_logging_removes_preflight_handler(
+    monkeypatch: pytest.MonkeyPatch,
+    tmp_path: Path,
+) -> None:
+    monkeypatch.delenv("STRIX_DEBUG", raising=False)
+    attach_preflight_logging()
+    assert _preflight_handlers("strix")
+
+    teardown = setup_scan_logging(tmp_path)
+    try:
+        for name in ("strix", "openai.agents"):
+            assert not _preflight_handlers(name)
+    finally:
+        teardown()