diff --git a/cmd/mattermost/commands/config.go b/cmd/mattermost/commands/config.go
index 273c52f262..6809c6172e 100644
--- a/cmd/mattermost/commands/config.go
+++ b/cmd/mattermost/commands/config.go
@@ -250,20 +250,8 @@ func configMigrateCmdF(command *cobra.Command, args []string) error {
 	from := args[0]
 	to := args[1]
 
-	// Get source config store - invalid config will throw error here
-	fromConfigStore, err := config.NewStore(from, false)
-	if err != nil {
-		return errors.Wrapf(err, "failed to access config %s", from)
-	}
+	err := config.Migrate(from, to)
 
-	// Get destination config store
-	toConfigStore, err := config.NewStore(to, false)
-	if err != nil {
-		return errors.Wrapf(err, "failed to access config %s", to)
-	}
-
-	// Copy config from source to destination
-	_, err = toConfigStore.Set(fromConfigStore.Get())
 	if err != nil {
 		return errors.Wrap(err, "failed to migrate config")
 	}
diff --git a/config/migrate.go b/config/migrate.go
new file mode 100644
index 0000000000..c6e9856e2c
--- /dev/null
+++ b/config/migrate.go
@@ -0,0 +1,52 @@
+// Copyright (c) 2015-present Mattermost, Inc. All Rights Reserved.
+// See License.txt for license information.
+
+package config
+
+import "github.com/pkg/errors"
+
+func Migrate(from, to string) error {
+	source, err := NewStore(from, false)
+	if err != nil {
+		return errors.Wrapf(err, "failed to access source config %s", from)
+	}
+
+	destination, err := NewStore(to, false)
+	if err != nil {
+		return errors.Wrapf(err, "failed to access destination config %s", to)
+	}
+
+	sourceConfig := source.Get()
+	if _, err = destination.Set(sourceConfig); err != nil {
+		return errors.Wrapf(err, "failed to set config")
+	}
+
+	files := []string{*sourceConfig.SamlSettings.IdpCertificateFile, *sourceConfig.SamlSettings.PublicCertificateFile,
+		*sourceConfig.SamlSettings.PrivateKeyFile}
+
+	for _, file := range files {
+		err = migrateFile(file, source, destination)
+
+		if err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
+func migrateFile(name string, source Store, destination Store) error {
+	fileExists, err := source.HasFile(name)
+	if err != nil {
+		return errors.Wrapf(err, "failed to check existence of %s", name)
+	}
+
+	if fileExists {
+		file, err := source.GetFile(name)
+		err = destination.SetFile(name, file)
+		if err != nil {
+			return errors.Wrapf(err, "failed to migrate %s", name)
+		}
+	}
+
+	return nil
+}
diff --git a/config/migrate_test.go b/config/migrate_test.go
new file mode 100644
index 0000000000..0560a7d01b
--- /dev/null
+++ b/config/migrate_test.go
@@ -0,0 +1,60 @@
+package config
+
+import (
+	"fmt"
+	"github.com/mattermost/mattermost-server/testlib"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"testing"
+)
+
+func TestMigrateDatabaseToFile(t *testing.T) {
+	helper := testlib.NewMainHelper()
+	sqlSettings := helper.GetSqlSettings()
+	sqlDSN := fmt.Sprintf("%s://%s", *sqlSettings.DriverName, *sqlSettings.DataSource)
+	fileDSN := "config.json"
+	files := []string{"IdpCertificateFile", "PublicCertificateFile", "PrivateKeyFile"}
+	data := make([]byte, 5)
+	ds, err := NewDatabaseStore(sqlDSN)
+	defer ds.Close()
+	require.NoError(t, err)
+	config := ds.Get()
+	config.SamlSettings.IdpCertificateFile = &files[0]
+	config.SamlSettings.PublicCertificateFile = &files[1]
+	config.SamlSettings.PrivateKeyFile = &files[2]
+	_, err = ds.Set(config)
+	require.NoError(t, err)
+
+	for _, file := range files {
+		err = ds.SetFile(file, data)
+		require.NoError(t, err)
+	}
+	err = Migrate(sqlDSN, fileDSN)
+	require.NoError(t, err)
+
+	fs, err := NewFileStore(fileDSN, false)
+	require.NoError(t, err)
+	defer fs.Close()
+
+	for _, file := range files {
+		hasFile, err := fs.HasFile(file)
+		require.NoError(t, err)
+		defer fs.RemoveFile(file)
+		assert.True(t, hasFile)
+	}
+
+	assert.Equal(t, ds.Get(), fs.Get())
+}
+
+func TestMigrateFileToDatabaseWhenFilePathIsNotSpecified(t *testing.T) {
+	helper := testlib.NewMainHelper()
+	sqlSettings := helper.GetSqlSettings()
+	sqlDSN := fmt.Sprintf("%s://%s", *sqlSettings.DriverName, *sqlSettings.DataSource)
+	fileDSN := "config.json"
+
+	_, err := NewFileStore(fileDSN, true)
+	require.NoError(t, err)
+
+	err = Migrate(fileDSN, sqlDSN)
+	require.NoError(t, err)
+}