diff --git a/Trigger/TriggerCommon/TriggerJobOpts/python/runHLT.py b/Trigger/TriggerCommon/TriggerJobOpts/python/runHLT.py
index 9c9fa80c460e5f8a452a68e806ae4cde9abee2d3..5dc2af271edc0a113d2219d8cae7fb2976aae241 100644
--- a/Trigger/TriggerCommon/TriggerJobOpts/python/runHLT.py
+++ b/Trigger/TriggerCommon/TriggerJobOpts/python/runHLT.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2002-2023 CERN for the benefit of the ATLAS collaboration
+# Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 """
 CA module to configure the (standalone) HLT for athena and athenaHLT.
 There is a separate entry point for each application to tailor some
@@ -120,6 +120,13 @@ def athenaHLTCfg(flags):
    # Set default flags for running HLT
    set_flags(flags)
 
+   # Decoding the flags from the command line is already done in athenaHLT.
+   # But we have to do it again in case some of the flags from set_flags
+   # get overwritten by the user.
+   from TrigPSC import PscConfig
+   for flag_arg in PscConfig.unparsedArguments:
+      flags.fillFromString(flag_arg)
+
    # Lock flags
    lock_and_restrict(flags)