diff --git a/.pytool/CISettings.py b/.pytool/CISettings.py
index b8b8080439..ec3beb0dcf 100644
--- a/.pytool/CISettings.py
+++ b/.pytool/CISettings.py
@@ -196,6 +196,12 @@ class Settings(CiBuildSettingsManager, UpdateSettingsManager, SetupSettingsManag
 
             try:
                 scopes += codeql_helpers.get_scopes(self.codeql)
+
+                if self.codeql:
+                    shell_environment.GetBuildVars().SetValue(
+                        "STUART_CODEQL_AUDIT_ONLY",
+                        "TRUE",
+                        "Set in CISettings.py")
             except NameError:
                 pass