diff --git a/daemon/config.go b/daemon/config.go
index e0b07b056d..c6f232d657 100644
--- a/daemon/config.go
+++ b/daemon/config.go
@@ -21,6 +21,15 @@ const (
 	disableNetworkBridge = "none"
 )
 
+// flatOptions contains configuration keys
+// that MUST NOT be parsed as deep structures.
+// Use this to differentiate these options
+// with others like the ones in CommonTLSOptions.
+var flatOptions = map[string]bool{
+	"cluster-store-opts": true,
+	"log-opts":           true,
+}
+
 // LogConfig represents the default log configuration.
 // It includes json tags to deserialize configuration from a file
 // using the same names that the flags in the command line uses.
@@ -208,13 +217,14 @@ func getConflictFreeConfiguration(configFile string, flags *flag.FlagSet) (*Conf
 func configValuesSet(config map[string]interface{}) map[string]interface{} {
 	flatten := make(map[string]interface{})
 	for k, v := range config {
-		if m, ok := v.(map[string]interface{}); ok {
+		if m, isMap := v.(map[string]interface{}); isMap && !flatOptions[k] {
 			for km, vm := range m {
 				flatten[km] = vm
 			}
-		} else {
-			flatten[k] = v
+			continue
 		}
+
+		flatten[k] = v
 	}
 	return flatten
 }
diff --git a/docker/daemon_test.go b/docker/daemon_test.go
index cd5d100d1a..5afdfb3bde 100644
--- a/docker/daemon_test.go
+++ b/docker/daemon_test.go
@@ -238,7 +238,7 @@ func TestLoadDaemonConfigWithEmbeddedOptions(t *testing.T) {
 		t.Fatal(err)
 	}
 	if loadedConfig == nil {
-		t.Fatalf("expected configuration %v, got nil", c)
+		t.Fatal("expected configuration, got nil")
 	}
 	if loadedConfig.CommonTLSOptions.CAFile != "/etc/certs/ca.pem" {
 		t.Fatalf("expected CA file path /etc/certs/ca.pem, got %v", loadedConfig.CommonTLSOptions.CAFile)
@@ -247,3 +247,47 @@ func TestLoadDaemonConfigWithEmbeddedOptions(t *testing.T) {
 		t.Fatalf("expected LogConfig type syslog, got %v", loadedConfig.LogConfig.Type)
 	}
 }
+
+func TestLoadDaemonConfigWithMapOptions(t *testing.T) {
+	c := &daemon.Config{}
+	common := &cli.CommonFlags{}
+	flags := mflag.NewFlagSet("test", mflag.ContinueOnError)
+
+	flags.Var(opts.NewNamedMapOpts("cluster-store-opts", c.ClusterOpts, nil), []string{"-cluster-store-opt"}, "")
+	flags.Var(opts.NewNamedMapOpts("log-opts", c.LogConfig.Config, nil), []string{"-log-opt"}, "")
+
+	f, err := ioutil.TempFile("", "docker-config-")
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	configFile := f.Name()
+	f.Write([]byte(`{
+		"cluster-store-opts": {"kv.cacertfile": "/var/lib/docker/discovery_certs/ca.pem"},
+		"log-opts": {"tag": "test"}
+}`))
+	f.Close()
+
+	loadedConfig, err := loadDaemonCliConfig(c, flags, common, configFile)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if loadedConfig == nil {
+		t.Fatal("expected configuration, got nil")
+	}
+	if loadedConfig.ClusterOpts == nil {
+		t.Fatal("expected cluster options, got nil")
+	}
+
+	expectedPath := "/var/lib/docker/discovery_certs/ca.pem"
+	if caPath := loadedConfig.ClusterOpts["kv.cacertfile"]; caPath != expectedPath {
+		t.Fatalf("expected %s, got %s", expectedPath, caPath)
+	}
+
+	if loadedConfig.LogConfig.Config == nil {
+		t.Fatal("expected log config options, got nil")
+	}
+	if tag := loadedConfig.LogConfig.Config["tag"]; tag != "test" {
+		t.Fatalf("expected log tag `test`, got %s", tag)
+	}
+}