diff --git a/config/config.go b/config/config.go
index e722a5cb..b382d2ef 100644
--- a/config/config.go
+++ b/config/config.go
@@ -401,15 +401,22 @@ func initConfig(fs *pflag.FlagSet) (cfg *Config, err error) {
 }
 
 func setupConfig(c *Config) {
-	// To show protofile and protopath field, set slice which has empty string
+	// To show protofile and protopath field in a config file, set slice which has empty string
 	// if these are nil. (please see default values.)
 	// Conversely, trim the empty string element when config loading.
-	if (c.Default.ProtoFile == nil) || (len(c.Default.ProtoFile) == 1 && c.Default.ProtoFile[0] == "") {
+	if c.Default.ProtoFile == nil {
 		c.Default.ProtoFile = []string{}
 	}
-	if (c.Default.ProtoPath == nil) || (len(c.Default.ProtoPath) == 1 && c.Default.ProtoPath[0] == "") {
+	if len(c.Default.ProtoFile) >= 1 && c.Default.ProtoFile[0] == "" {
+		c.Default.ProtoFile = c.Default.ProtoFile[1:]
+	}
+
+	if c.Default.ProtoPath == nil {
 		c.Default.ProtoPath = []string{}
 	}
+	if len(c.Default.ProtoPath) >= 1 && c.Default.ProtoPath[0] == "" {
+		c.Default.ProtoPath = c.Default.ProtoPath[1:]
+	}
 }
 
 // Edit opens the project local config file with an editor.
diff --git a/config/config_test.go b/config/config_test.go
index 26941984..55540b7a 100644
--- a/config/config_test.go
+++ b/config/config_test.go
@@ -163,14 +163,14 @@ func TestMain(m *testing.M) {
 
 func TestLoad(t *testing.T) {
 	checkValues := func(t *testing.T, c *Config) {
-		if len(c.Default.ProtoFile) == 1 {
+		if len(c.Default.ProtoFile) >= 1 {
 			if len(c.Default.ProtoFile[0]) == 0 {
-				t.Fatalf("Default.ProtoFile must not empty")
+				t.Fatalf("Default.ProtoFile must not be empty")
 			}
 		}
-		if len(c.Default.ProtoPath) == 1 {
+		if len(c.Default.ProtoPath) >= 1 {
 			if len(c.Default.ProtoPath[0]) == 0 {
-				t.Fatalf("Default.ProtoPath must not empty")
+				t.Fatalf("Default.ProtoPath must not be empty")
 			}
 		}
 	}
@@ -294,6 +294,21 @@ func TestLoad(t *testing.T) {
 
 		return cfg
 	})
+
+	assertWithGolden(t, "apply some proto files and paths", func(t *testing.T) *Config {
+		_, _, cleanup := setupEnv(t)
+		defer cleanup()
+
+		fs := pflag.NewFlagSet("test", pflag.ExitOnError)
+		fs.StringSlice("path", []string{"foo", "bar"}, "")
+		fs.StringSlice("proto", []string{"hoge", "fuga"}, "")
+
+		cfg := mustGet(t, fs)
+
+		checkValues(t, cfg)
+
+		return cfg
+	})
 }
 
 func TestEdit(t *testing.T) {
diff --git a/config/testdata/fixtures/apply_some_proto_files_and_paths.golden.toml b/config/testdata/fixtures/apply_some_proto_files_and_paths.golden.toml
new file mode 100644
index 00000000..c5ba5beb
--- /dev/null
+++ b/config/testdata/fixtures/apply_some_proto_files_and_paths.golden.toml
@@ -0,0 +1,38 @@
+
+[default]
+  package = ""
+  protofile = []
+  protopath = ["foo","bar"]
+  service = ""
+
+[log]
+  prefix = "evans: "
+
+[meta]
+  autoupdate = false
+  configversion = "0.6.10"
+  updatelevel = "patch"
+
+[repl]
+  coloredoutput = true
+  historysize = 100
+  inputpromptformat = "{ancestor}{name} ({type}) => "
+  promptformat = "{package}.{service}@{addr}:{port}"
+  silent = false
+  splashtextpath = ""
+
+[request]
+  cacertfile = ""
+  certfile = ""
+  certkeyfile = ""
+  web = false
+
+  [request.header]
+    grpc-client = ["evans"]
+
+[server]
+  host = "127.0.0.1"
+  name = ""
+  port = "50051"
+  reflection = false
+  tls = false