diff --git a/x-pack/osquerybeat/beater/osquery_runner.go b/x-pack/osquerybeat/beater/osquery_runner.go
index a1c890a559d..bd426f1eb13 100644
--- a/x-pack/osquerybeat/beater/osquery_runner.go
+++ b/x-pack/osquerybeat/beater/osquery_runner.go
@@ -68,11 +68,11 @@ func (r *osqueryRunner) Run(parentCtx context.Context, runfn osqueryRunFunc) err
 
 			// Wait until osquery runner exists
 			wg.Wait()
-
-			// Set the flags to use
-			flags = newFlags
 		}
 
+		// Set the flags to use
+		flags = newFlags
+
 		// Start osqueryd if not running
 		if cn == nil {
 			r.log.Info("Start osqueryd")