diff --git a/scripts/supybot-plugin-doc b/scripts/supybot-plugin-doc
index eb2cb4625..e9081757b 100644
--- a/scripts/supybot-plugin-doc
+++ b/scripts/supybot-plugin-doc
@@ -35,6 +35,7 @@ import os
 import sys
 import shutil
 import string
+import logging
 
 import supybot
 
@@ -340,6 +341,10 @@ if __name__ == '__main__':
         genDoc(Plugin, options)
 
     if options.clean:
+        # We are about to remove the log dir; so trying to write anything
+        # (such as "Shutdown initiated." and friends, from atexit callbacks)
+        # would result in errors.
+        log._handler.setLevel(logging.CRITICAL)
         shutil.rmtree(conf.supybot.directories.log())
         shutil.rmtree(conf.supybot.directories.conf())
         shutil.rmtree(conf.supybot.directories.data())