diff --git a/CHANGELOG.md b/CHANGELOG.md
index 898ed3fcb5e1..65ed01309a2c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,6 +54,8 @@ Main (unreleased)
   each time it pulls. (@erikbaranowski)
 
 - Allow overriding default `User-Agent` for `http.remote` component (@hainenber)
+- Fix panic when running `grafana-agentctl config-check` against config files
+  having `integrations` block (both V1 and V2). (@hainenber)
 
 - Fix a deadlock candidate in the `loki.process` component. (@tpaschalis)
 
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index 880f5e667759..a10b47b81e96 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -522,3 +522,26 @@ func TestConfig_EmptyServerConfigFails(t *testing.T) {
 	_, err := Load(fs, []string{"--config.file", "./testdata/server_empty.yml"}, logger)
 	require.Error(t, err)
 }
+
+func TestConfig_ValidateConfigWithIntegrationV1(t *testing.T) {
+	input := util.Untab(`
+integrations:
+	agent:
+		enabled: true
+`)
+	var cfg Config
+	require.NoError(t, LoadBytes([]byte(input), false, &cfg))
+	require.NoError(t, cfg.Validate(nil))
+}
+
+func TestConfig_ValidateConfigWithIntegrationV2(t *testing.T) {
+	input := util.Untab(`
+integrations:
+	agent:
+		autoscrape:
+			enabled: true
+`)
+	var cfg Config
+	require.NoError(t, LoadBytes([]byte(input), false, &cfg))
+	require.NoError(t, cfg.Validate(nil))
+}
diff --git a/pkg/config/integrations.go b/pkg/config/integrations.go
index e62ac5e96e4f..acf76492aff3 100644
--- a/pkg/config/integrations.go
+++ b/pkg/config/integrations.go
@@ -85,10 +85,15 @@ func (c VersionedIntegrations) IsZero() bool {
 
 // ApplyDefaults applies defaults to the subsystem based on globals.
 func (c *VersionedIntegrations) ApplyDefaults(sflags *server.Flags, mcfg *metrics.Config) error {
-	if c.version != integrationsVersion2 {
+	switch {
+	case c.version != integrationsVersion2 && c.ConfigV1 != nil:
 		return c.ConfigV1.ApplyDefaults(sflags, mcfg)
+	case c.configV2 != nil:
+		return c.configV2.ApplyDefaults(mcfg)
+	default:
+		// No-op
+		return nil
 	}
-	return c.configV2.ApplyDefaults(mcfg)
 }
 
 // setVersion completes the deferred unmarshal and unmarshals the raw YAML into