diff --git a/pkg/commands/fmt.go b/pkg/commands/fmt.go
index cb7472847f25..66ba197f05f6 100644
--- a/pkg/commands/fmt.go
+++ b/pkg/commands/fmt.go
@@ -89,6 +89,10 @@ func (c *fmtCommand) persistentPreRunE(cmd *cobra.Command, args []string) error
 }
 
 func (c *fmtCommand) preRunE(_ *cobra.Command, _ []string) error {
+	if c.cfg.GetConfigDir() != "" && c.cfg.Version != "2" {
+		return fmt.Errorf("invalid version of the configuration: %q", c.cfg.Version)
+	}
+
 	metaFormatter, err := goformatters.NewMetaFormatter(c.log, &c.cfg.Formatters, &c.cfg.Run)
 	if err != nil {
 		return fmt.Errorf("failed to create meta-formatter: %w", err)
diff --git a/pkg/commands/run.go b/pkg/commands/run.go
index 76735afe9384..20ff2df9a0d3 100644
--- a/pkg/commands/run.go
+++ b/pkg/commands/run.go
@@ -185,6 +185,10 @@ func (c *runCommand) persistentPostRunE(_ *cobra.Command, _ []string) error {
 }
 
 func (c *runCommand) preRunE(_ *cobra.Command, args []string) error {
+	if c.cfg.GetConfigDir() != "" && c.cfg.Version != "2" {
+		return fmt.Errorf("invalid version of the configuration: %q", c.cfg.Version)
+	}
+
 	dbManager, err := lintersdb.NewManager(c.log.Child(logutils.DebugKeyLintersDB), c.cfg,
 		lintersdb.NewLinterBuilder(), lintersdb.NewPluginModuleBuilder(c.log), lintersdb.NewPluginGoBuilder(c.log))
 	if err != nil {
diff --git a/test/run_test.go b/test/run_test.go
index 67344d9d82c0..5267764fbb39 100644
--- a/test/run_test.go
+++ b/test/run_test.go
@@ -30,10 +30,11 @@ func TestAutogeneratedNoIssues(t *testing.T) {
 	binPath := testshared.InstallGolangciLint(t)
 
 	cfg := `
-				linters:
-					exclusions:
-						generated: lax
-			`
+version: "2"
+linters:
+	exclusions:
+		generated: lax
+`
 
 	testshared.NewRunnerBuilder(t).
 		WithConfig(cfg).
@@ -96,9 +97,10 @@ func TestTimeoutInConfig(t *testing.T) {
 	binPath := testshared.InstallGolangciLint(t)
 
 	cfg := `
-				run:
-					timeout: 1ms
-			`
+version: "2"
+run:
+	timeout: 1ms
+`
 
 	// Run with disallowed option set only in config
 	testshared.NewRunnerBuilder(t).
@@ -331,11 +333,12 @@ func TestUnsafeOk(t *testing.T) {
 	binPath := testshared.InstallGolangciLint(t)
 
 	cfg := `
-				linters:
-					exclusions:
-						presets:
-						- common-false-positives
-			`
+version: "2"
+linters:
+	exclusions:
+		presets:
+		- common-false-positives
+`
 
 	testshared.NewRunnerBuilder(t).
 		WithConfig(cfg).