diff --git a/CHANGES.rst b/CHANGES.rst
index 0ab9f54f8..9f0a451d9 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -22,7 +22,11 @@ This list is detailed and covers changes in each pre-release version.
 Unreleased
 ----------
 
-Nothing yet.
+- Fix: a signal handler was being set from multiple threads, causing an error:
+  ``ValueError: signal only works in main thread``.  This is now fixed, closing
+  `issue 1312`_.
+
+.. _issue 1312: https://github.com/nedbat/coveragepy/issues/1312
 
 
 .. _changes_63:
diff --git a/coverage/control.py b/coverage/control.py
index 0f62198a6..9dfa59fb1 100644
--- a/coverage/control.py
+++ b/coverage/control.py
@@ -11,6 +11,7 @@
 import platform
 import signal
 import sys
+import threading
 import time
 import warnings
 
@@ -528,8 +529,10 @@ def _init_for_start(self):
         # It's useful to write debug info after initing for start.
         self._should_write_debug = True
 
+        # Register our clean-up handlers.
         atexit.register(self._atexit)
-        if not env.WINDOWS:
+        is_main = (threading.current_thread() == threading.main_thread())
+        if is_main and not env.WINDOWS:
             # The Python docs seem to imply that SIGTERM works uniformly even
             # on Windows, but that's not my experience, and this agrees:
             # https://stackoverflow.com/questions/35772001/x/35792192#35792192