diff --git a/dgraph/cmd/root.go b/dgraph/cmd/root.go
index 6df198cd997..7c7ce70f6e5 100644
--- a/dgraph/cmd/root.go
+++ b/dgraph/cmd/root.go
@@ -127,11 +127,14 @@ func initCmds() {
 			x.CheckfNoTrace(os.Chdir(cwd))
 		}
 
-		cfg := rootConf.GetString("config")
-		if cfg == "" {
-			return
-		}
 		for _, sc := range subcommands {
+			// Set config file is provided for each subcommand, this is done
+			// for individual subcommand because each subcommand has its own config
+			// prefix, like `dgraph zero` expects the prefix to be `DGRAPH_ZERO`.
+			cfg := sc.Conf.GetString("config")
+			if cfg == "" {
+				continue
+			}
 			sc.Conf.SetConfigFile(cfg)
 			x.Check(errors.Wrapf(sc.Conf.ReadInConfig(), "reading config"))
 			setGlogFlags(sc.Conf)