diff --git a/cmd/ipfs/daemon.go b/cmd/ipfs/daemon.go
index 25b69b34065e..020a99a37576 100644
--- a/cmd/ipfs/daemon.go
+++ b/cmd/ipfs/daemon.go
@@ -233,20 +233,24 @@ func daemonFunc(req *cmds.Request, re cmds.ResponseEmitter, env cmds.Environment
 	// first, whether user has provided the initialization flag. we may be
 	// running in an uninitialized state.
 	initialize, _ := req.Options[initOptionKwd].(bool)
-	if initialize && !fsrepo.IsInitialized(cctx.ConfigRoot) {
-		cfgLocation, _ := req.Options[initConfigOptionKwd].(string)
-		profiles, _ := req.Options[initProfileOptionKwd].(string)
-		var conf *config.Config
+	if initialize {
+		if fsrepo.IsInitialized(cctx.ConfigRoot) {
+			log.Warningf("repo is already initialized, nothing will be altered")
+		} else {
+			cfgLocation, _ := req.Options[initConfigOptionKwd].(string)
+			profiles, _ := req.Options[initProfileOptionKwd].(string)
+			var conf *config.Config
+
+			if cfgLocation != "" {
+				if conf, err = cserial.Load(cfgLocation); err != nil {
+					return err
+				}
+			}
 
-		if cfgLocation != "" {
-			if conf, err = cserial.Load(cfgLocation); err != nil {
+			if err = doInit(os.Stdout, cctx.ConfigRoot, false, nBitsForKeypairDefault, profiles, conf); err != nil {
 				return err
 			}
 		}
-
-		if err = doInit(os.Stdout, cctx.ConfigRoot, false, nBitsForKeypairDefault, profiles, conf); err != nil {
-			return err
-		}
 	}
 
 	// acquire the repo lock _before_ constructing a node. we need to make