diff --git a/coremain/run.go b/coremain/run.go
index 61d2e24be..23d5d5f7e 100644
--- a/coremain/run.go
+++ b/coremain/run.go
@@ -18,20 +18,6 @@ import (
 )
 
 func init() {
-	// Reset flag.CommandLine to get rid of unwanted flags for instance from glog (used in kubernetes).
-	// And readd the once we want to keep.
-	flag.VisitAll(func(f *flag.Flag) {
-		if _, ok := flagsBlacklist[f.Name]; ok {
-			return
-		}
-		flagsToKeep = append(flagsToKeep, f)
-	})
-
-	flag.CommandLine = flag.NewFlagSet(os.Args[0], flag.ExitOnError)
-	for _, f := range flagsToKeep {
-		flag.Var(f.Value, f.Name, f.Usage)
-	}
-
 	caddy.TrapSignals()
 	caddy.DefaultConfigFile = "Corefile"
 	caddy.Quiet = true // don't show init stuff from caddy
@@ -54,6 +40,19 @@ func init() {
 
 // Run is CoreDNS's main() function.
 func Run() {
+	// Reset flag.CommandLine to get rid of unwanted flags for instance from glog (used in kubernetes).
+	// And readd the once we want to keep.
+	flag.VisitAll(func(f *flag.Flag) {
+		if _, ok := flagsBlacklist[f.Name]; ok {
+			return
+		}
+		flagsToKeep = append(flagsToKeep, f)
+	})
+
+	flag.CommandLine = flag.NewFlagSet(os.Args[0], flag.ExitOnError)
+	for _, f := range flagsToKeep {
+		flag.Var(f.Value, f.Name, f.Usage)
+	}
 
 	flag.Parse()