diff --git a/pkg/lint2/discovery.go b/pkg/lint2/discovery.go
index 639bc1a7e..ad34e30b8 100644
--- a/pkg/lint2/discovery.go
+++ b/pkg/lint2/discovery.go
@@ -174,6 +174,44 @@ func hasKind(path string, kind string) (bool, error) {
 	return false, nil
 }
 
+// hasAPIVersionKind checks if a YAML file contains a specific apiVersion and kind.
+// Handles multi-document YAML files properly using yaml.NewDecoder.
+// For files with syntax errors, falls back to simple regex matching to detect both apiVersion and kind.
+func hasAPIVersionKind(path string, apiVersion string, kind string) (bool, error) {
+	data, err := os.ReadFile(path)
+	if err != nil {
+		return false, err
+	}
+
+	decoder := yaml.NewDecoder(bytes.NewReader(data))
+
+	for {
+		var doc struct {
+			Kind       string `yaml:"kind"`
+			APIVersion string `yaml:"apiVersion"`
+		}
+
+		err := decoder.Decode(&doc)
+		if err != nil {
+			if err == io.EOF {
+				break
+			}
+			// Parse error - fall back to regex matching
+			kindPattern := fmt.Sprintf(`(?m)^kind:\s+%s\s*$`, regexp.QuoteMeta(kind))
+			apiPattern := fmt.Sprintf(`(?m)^apiVersion:\s+%s\s*$`, regexp.QuoteMeta(apiVersion))
+			kindMatched, _ := regexp.Match(kindPattern, data)
+			apiMatched, _ := regexp.Match(apiPattern, data)
+			return kindMatched && apiMatched, nil
+		}
+
+		if doc.Kind == kind && doc.APIVersion == apiVersion {
+			return true, nil
+		}
+	}
+
+	return false, nil
+}
+
 // discoverPreflightPaths discovers Preflight spec files from a glob pattern.
 // This is a thin wrapper around discoverYAMLsByKind for backward compatibility.
 //
diff --git a/pkg/lint2/discovery_test.go b/pkg/lint2/discovery_test.go
index 25acf7098..303bda5ff 100644
--- a/pkg/lint2/discovery_test.go
+++ b/pkg/lint2/discovery_test.go
@@ -2676,3 +2676,143 @@ func TestDiscoverSupportBundlePaths_ExplicitBypass(t *testing.T) {
 		t.Errorf("Expected bundle in dist/, got: %s", bundles[0])
 	}
 }
+
+// Phase 9 Tests: hasAPIVersionKind
+
+func TestHasAPIVersionKind_ECConfigMatch(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "ec.yaml")
+	content := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if !got {
+		t.Errorf("hasAPIVersionKind() = false, want true for EC Config")
+	}
+}
+
+func TestHasAPIVersionKind_KOTSConfigMismatch(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "config.yaml")
+	content := `apiVersion: kots.io/v1beta1
+kind: Config
+metadata:
+  name: config
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if got {
+		t.Errorf("hasAPIVersionKind() = true, want false for KOTS Config")
+	}
+}
+
+func TestHasAPIVersionKind_MultiDocumentWithECConfig(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "multi.yaml")
+	content := `apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: cm
+---
+apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if !got {
+		t.Errorf("hasAPIVersionKind() = false, want true for multi-doc with EC Config")
+	}
+}
+
+func TestHasAPIVersionKind_MultiDocumentWithoutECConfig(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "multi.yaml")
+	content := `apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: cm
+---
+apiVersion: kots.io/v1beta1
+kind: Config
+metadata:
+  name: config
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if got {
+		t.Errorf("hasAPIVersionKind() = true, want false for multi-doc without EC Config")
+	}
+}
+
+func TestHasAPIVersionKind_EmptyFile(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "empty.yaml")
+	if err := os.WriteFile(path, []byte(""), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if got {
+		t.Errorf("hasAPIVersionKind() = true, want false for empty file")
+	}
+}
+
+func TestHasAPIVersionKind_InvalidYAMLRegexFallback(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "invalid.yaml")
+	content := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: my-app
+          chartVersion: 1.2.3
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	got, err := hasAPIVersionKind(path, "embeddedcluster.replicated.com/v1beta1", "Config")
+	if err != nil {
+		t.Fatalf("hasAPIVersionKind() error = %v", err)
+	}
+	if !got {
+		t.Errorf("hasAPIVersionKind() = false, want true for valid EC Config")
+	}
+}
diff --git a/pkg/lint2/helmchart.go b/pkg/lint2/helmchart.go
index 70a606d8d..01410fce1 100644
--- a/pkg/lint2/helmchart.go
+++ b/pkg/lint2/helmchart.go
@@ -121,6 +121,22 @@ func DiscoverHelmChartManifests(manifestGlobs []string) (map[string]*HelmChartMa
 		}
 	}
 
+	// Discover EC Config helm charts and merge
+	ecHelmCharts, err := DiscoverECConfigHelmCharts(manifestGlobs)
+	if err != nil {
+		return nil, err
+	}
+	for key, manifest := range ecHelmCharts {
+		if existing, found := helmCharts[key]; found {
+			return nil, &DuplicateHelmChartError{
+				ChartKey:   key,
+				FirstFile:  existing.FilePath,
+				SecondFile: manifest.FilePath,
+			}
+		}
+		helmCharts[key] = manifest
+	}
+
 	// Return empty map if no HelmCharts found - validation layer will check if charts need HelmCharts
 	// Discovery is lenient - validation happens later in the flow
 	if len(helmCharts) == 0 {
@@ -136,6 +152,71 @@ func isHelmChartManifest(path string) (bool, error) {
 	return hasKind(path, "HelmChart")
 }
 
+// DiscoverECConfigHelmCharts scans manifest glob patterns and extracts helm chart
+// declarations from embeddedcluster.replicated.com/v1beta1 Config manifests.
+// It returns a map keyed by "name:chartVersion" for efficient lookup during validation.
+//
+// Silently skips:
+//   - Files that can't be read
+//   - Files that aren't valid YAML
+//   - Files that don't contain an EC Config with extensions.helmCharts
+//   - Hidden directories (.git, .github, etc.)
+func DiscoverECConfigHelmCharts(manifestGlobs []string) (map[string]*HelmChartManifest, error) {
+	if len(manifestGlobs) == 0 {
+		return make(map[string]*HelmChartManifest), nil
+	}
+
+	helmCharts := make(map[string]*HelmChartManifest)
+	seenFiles := make(map[string]bool)
+
+	for _, pattern := range manifestGlobs {
+		matches, err := GlobFiles(pattern)
+		if err != nil {
+			return nil, fmt.Errorf("failed to expand manifest pattern %s: %w", pattern, err)
+		}
+
+		for _, path := range matches {
+			if isHiddenPath(path) {
+				continue
+			}
+			if seenFiles[path] {
+				continue
+			}
+			seenFiles[path] = true
+
+			// Quick apiVersion+kind check before parsing to avoid matching KOTS Config
+			isECConfig, err := hasAPIVersionKind(path, ecConfigAPIVersion, "Config")
+			if err != nil || !isECConfig {
+				continue
+			}
+
+			// Parse EC Config helm charts
+			manifests, err := parseECConfigHelmCharts(path)
+			if err != nil {
+				continue
+			}
+
+			for _, manifest := range manifests {
+				key := fmt.Sprintf("%s:%s", manifest.Name, manifest.ChartVersion)
+				if existing, found := helmCharts[key]; found {
+					return nil, &DuplicateHelmChartError{
+						ChartKey:   key,
+						FirstFile:  existing.FilePath,
+						SecondFile: manifest.FilePath,
+					}
+				}
+				helmCharts[key] = manifest
+			}
+		}
+	}
+
+	if len(helmCharts) == 0 {
+		return make(map[string]*HelmChartManifest), nil
+	}
+
+	return helmCharts, nil
+}
+
 // parseHelmChartManifest parses a HelmChart manifest and extracts the fields needed for preflight rendering.
 // Accepts any apiVersion (validation happens in the linter).
 //
@@ -150,25 +231,23 @@ func parseHelmChartManifest(path string) (*HelmChartManifest, error) {
 		return nil, fmt.Errorf("failed to read file: %w", err)
 	}
 
-	// Parse the full HelmChart structure
-	// Support both v1beta1 and v1beta2 - they have the same structure for fields we need
-	var helmChart struct {
-		APIVersion string `yaml:"apiVersion"`
-		Kind       string `yaml:"kind"`
-		Spec       struct {
-			Chart struct {
-				Name         string `yaml:"name"`
-				ChartVersion string `yaml:"chartVersion"`
-			} `yaml:"chart"`
-			Builder map[string]interface{} `yaml:"builder"`
-		} `yaml:"spec"`
-	}
-
 	// Use yaml.NewDecoder to handle multi-document files
 	decoder := yaml.NewDecoder(bytes.NewReader(data))
 
 	// Find the first HelmChart document
 	for {
+		var helmChart struct {
+			APIVersion string `yaml:"apiVersion"`
+			Kind       string `yaml:"kind"`
+			Spec       struct {
+				Chart struct {
+					Name         string `yaml:"name"`
+					ChartVersion string `yaml:"chartVersion"`
+				} `yaml:"chart"`
+				Builder map[string]interface{} `yaml:"builder"`
+			} `yaml:"spec"`
+		}
+
 		err := decoder.Decode(&helmChart)
 		if err != nil {
 			if err == io.EOF {
@@ -178,26 +257,79 @@ func parseHelmChartManifest(path string) (*HelmChartManifest, error) {
 		}
 
 		if helmChart.Kind == "HelmChart" {
-			break
+			// Validate required fields
+			if helmChart.Spec.Chart.Name == "" {
+				return nil, fmt.Errorf("spec.chart.name is required but not found")
+			}
+			if helmChart.Spec.Chart.ChartVersion == "" {
+				return nil, fmt.Errorf("spec.chart.chartVersion is required but not found")
+			}
+
+			// Note: We don't validate apiVersion here - discovery is permissive.
+			// The preflight linter will validate apiVersion when it processes the HelmChart.
+			// This allows future apiVersions to work without code changes.
+
+			return &HelmChartManifest{
+				Name:          helmChart.Spec.Chart.Name,
+				ChartVersion:  helmChart.Spec.Chart.ChartVersion,
+				BuilderValues: helmChart.Spec.Builder, // Can be nil or empty - that's valid
+				FilePath:      path,
+			}, nil
 		}
 	}
+}
 
-	// Validate required fields
-	if helmChart.Spec.Chart.Name == "" {
-		return nil, fmt.Errorf("spec.chart.name is required but not found")
-	}
-	if helmChart.Spec.Chart.ChartVersion == "" {
-		return nil, fmt.Errorf("spec.chart.chartVersion is required but not found")
+// parseECConfigHelmCharts reads a YAML file and extracts helm chart declarations from
+// any embeddedcluster.replicated.com/v1beta1 Config documents.
+// It returns a slice of HelmChartManifest (without BuilderValues, as EC Config doesn't have them).
+func parseECConfigHelmCharts(path string) ([]*HelmChartManifest, error) {
+	data, err := os.ReadFile(path)
+	if err != nil {
+		return nil, fmt.Errorf("failed to read file: %w", err)
 	}
 
-	// Note: We don't validate apiVersion here - discovery is permissive.
-	// The preflight linter will validate apiVersion when it processes the HelmChart.
-	// This allows future apiVersions to work without code changes.
+	decoder := yaml.NewDecoder(bytes.NewReader(data))
+	var manifests []*HelmChartManifest
+
+	for {
+		var ecConfig struct {
+			APIVersion string `yaml:"apiVersion"`
+			Kind       string `yaml:"kind"`
+			Spec       struct {
+				Extensions struct {
+					HelmCharts []struct {
+						Chart struct {
+							Name         string `yaml:"name"`
+							ChartVersion string `yaml:"chartVersion"`
+						} `yaml:"chart"`
+					} `yaml:"helmCharts"`
+				} `yaml:"extensions"`
+			} `yaml:"spec"`
+		}
+
+		err := decoder.Decode(&ecConfig)
+		if err != nil {
+			if err == io.EOF {
+				break
+			}
+			return nil, fmt.Errorf("failed to parse YAML: %w", err)
+		}
+
+		if ecConfig.Kind != "Config" || ecConfig.APIVersion != ecConfigAPIVersion {
+			continue
+		}
+
+		for _, hc := range ecConfig.Spec.Extensions.HelmCharts {
+			if hc.Chart.Name == "" || hc.Chart.ChartVersion == "" {
+				continue
+			}
+			manifests = append(manifests, &HelmChartManifest{
+				Name:         hc.Chart.Name,
+				ChartVersion: hc.Chart.ChartVersion,
+				FilePath:     path,
+			})
+		}
+	}
 
-	return &HelmChartManifest{
-		Name:          helmChart.Spec.Chart.Name,
-		ChartVersion:  helmChart.Spec.Chart.ChartVersion,
-		BuilderValues: helmChart.Spec.Builder, // Can be nil or empty - that's valid
-		FilePath:      path,
-	}, nil
+	return manifests, nil
 }
diff --git a/pkg/lint2/helmchart_test.go b/pkg/lint2/helmchart_test.go
index 447526dd2..5ac258ec4 100644
--- a/pkg/lint2/helmchart_test.go
+++ b/pkg/lint2/helmchart_test.go
@@ -754,3 +754,232 @@ spec:
 		}
 	})
 }
+
+func TestDiscoverECConfigHelmCharts(t *testing.T) {
+	t.Run("empty manifests list returns empty map", func(t *testing.T) {
+		manifests, err := DiscoverECConfigHelmCharts([]string{})
+		if err != nil {
+			t.Fatalf("unexpected error for empty manifests list: %v", err)
+		}
+		if manifests == nil {
+			t.Fatal("expected non-nil map, got nil")
+		}
+		if len(manifests) != 0 {
+			t.Errorf("expected empty map, got %d manifests", len(manifests))
+		}
+	})
+
+	t.Run("single valid EC Config helm chart", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		ecFile := filepath.Join(tmpDir, "ec.yaml")
+		content := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: my-app
+          chartVersion: 1.2.3
+`
+		if err := os.WriteFile(ecFile, []byte(content), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		pattern := filepath.Join(tmpDir, "*.yaml")
+		manifests, err := DiscoverECConfigHelmCharts([]string{pattern})
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+
+		if len(manifests) != 1 {
+			t.Fatalf("expected 1 manifest, got %d", len(manifests))
+		}
+
+		key := "my-app:1.2.3"
+		manifest, found := manifests[key]
+		if !found {
+			t.Fatalf("expected manifest with key %q not found", key)
+		}
+		if manifest.Name != "my-app" {
+			t.Errorf("expected name 'my-app', got %q", manifest.Name)
+		}
+		if manifest.ChartVersion != "1.2.3" {
+			t.Errorf("expected chartVersion '1.2.3', got %q", manifest.ChartVersion)
+		}
+		if manifest.FilePath != ecFile {
+			t.Errorf("expected filePath %q, got %q", ecFile, manifest.FilePath)
+		}
+	})
+
+	t.Run("multiple EC Config helm charts", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		ecFile := filepath.Join(tmpDir, "ec.yaml")
+		content := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: app-one
+          chartVersion: 1.0.0
+      - chart:
+          name: app-two
+          chartVersion: 2.0.0
+`
+		if err := os.WriteFile(ecFile, []byte(content), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		pattern := filepath.Join(tmpDir, "*.yaml")
+		manifests, err := DiscoverECConfigHelmCharts([]string{pattern})
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+
+		if len(manifests) != 2 {
+			t.Fatalf("expected 2 manifests, got %d", len(manifests))
+		}
+
+		if _, found := manifests["app-one:1.0.0"]; !found {
+			t.Error("expected app-one:1.0.0 not found")
+		}
+		if _, found := manifests["app-two:2.0.0"]; !found {
+			t.Error("expected app-two:2.0.0 not found")
+		}
+	})
+
+	t.Run("duplicate EC Config helm charts returns error", func(t *testing.T) {
+		tmpDir := t.TempDir()
+
+		ecFile1 := filepath.Join(tmpDir, "ec1.yaml")
+		content1 := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec1
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: my-app
+          chartVersion: 1.0.0
+`
+		if err := os.WriteFile(ecFile1, []byte(content1), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		ecFile2 := filepath.Join(tmpDir, "ec2.yaml")
+		content2 := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec2
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: my-app
+          chartVersion: 1.0.0
+`
+		if err := os.WriteFile(ecFile2, []byte(content2), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		pattern := filepath.Join(tmpDir, "*.yaml")
+		_, err := DiscoverECConfigHelmCharts([]string{pattern})
+		if err == nil {
+			t.Fatal("expected error for duplicate EC Config helm chart, got nil")
+		}
+
+		dupErr, ok := err.(*DuplicateHelmChartError)
+		if !ok {
+			t.Fatalf("expected DuplicateHelmChartError, got %T", err)
+		}
+		if dupErr.ChartKey != "my-app:1.0.0" {
+			t.Errorf("expected ChartKey 'my-app:1.0.0', got %q", dupErr.ChartKey)
+		}
+	})
+
+	t.Run("non-EC Config files skipped", func(t *testing.T) {
+		tmpDir := t.TempDir()
+
+		kotsConfig := filepath.Join(tmpDir, "config.yaml")
+		kotsContent := `apiVersion: kots.io/v1beta1
+kind: Config
+metadata:
+  name: config
+spec:
+  groups: []
+`
+		if err := os.WriteFile(kotsConfig, []byte(kotsContent), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		pattern := filepath.Join(tmpDir, "*.yaml")
+		manifests, err := DiscoverECConfigHelmCharts([]string{pattern})
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+		if len(manifests) != 0 {
+			t.Errorf("expected 0 manifests, got %d", len(manifests))
+		}
+	})
+
+	t.Run("merged with kots HelmCharts in DiscoverHelmChartManifests", func(t *testing.T) {
+		tmpDir := t.TempDir()
+
+		helmChartFile := filepath.Join(tmpDir, "helmchart.yaml")
+		helmContent := `apiVersion: kots.io/v1beta1
+kind: HelmChart
+metadata:
+  name: kots-chart
+spec:
+  chart:
+    name: kots-app
+    chartVersion: 1.0.0
+`
+		if err := os.WriteFile(helmChartFile, []byte(helmContent), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		ecFile := filepath.Join(tmpDir, "ec.yaml")
+		ecContent := `apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: ec-app
+          chartVersion: 2.0.0
+`
+		if err := os.WriteFile(ecFile, []byte(ecContent), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		pattern := filepath.Join(tmpDir, "*.yaml")
+		manifests, err := DiscoverHelmChartManifests([]string{pattern})
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+
+		if len(manifests) != 2 {
+			t.Fatalf("expected 2 manifests (1 kots + 1 EC), got %d", len(manifests))
+		}
+
+		if _, found := manifests["kots-app:1.0.0"]; !found {
+			t.Error("expected kots-app:1.0.0 not found")
+		}
+		if _, found := manifests["ec-app:2.0.0"]; !found {
+			t.Error("expected ec-app:2.0.0 not found")
+		}
+	})
+}
diff --git a/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/.replicated b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/.replicated
new file mode 100644
index 000000000..41bcca854
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/.replicated
@@ -0,0 +1,4 @@
+charts:
+  - path: ./chart
+manifests:
+  - ./manifests/*.yaml
diff --git a/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/Chart.yaml b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/Chart.yaml
new file mode 100644
index 000000000..3dafca10c
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: ec-app
+version: 1.0.0
+description: Test chart for EC Config validation scenario
diff --git a/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/values.yaml b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/values.yaml
new file mode 100644
index 000000000..d6c93d3e8
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/chart/values.yaml
@@ -0,0 +1 @@
+# default values
diff --git a/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/manifests/ec.yaml b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/manifests/ec.yaml
new file mode 100644
index 000000000..ff59aba4a
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-7-ec-config-helmcharts/manifests/ec.yaml
@@ -0,0 +1,11 @@
+apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: ec-app
+          chartVersion: 1.0.0
diff --git a/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/.replicated b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/.replicated
new file mode 100644
index 000000000..41bcca854
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/.replicated
@@ -0,0 +1,4 @@
+charts:
+  - path: ./chart
+manifests:
+  - ./manifests/*.yaml
diff --git a/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/Chart.yaml b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/Chart.yaml
new file mode 100644
index 000000000..986fbf040
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: other-app
+version: 1.0.0
+description: Test chart with matching kots HelmChart manifest
diff --git a/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/values.yaml b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/values.yaml
new file mode 100644
index 000000000..d6c93d3e8
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/chart/values.yaml
@@ -0,0 +1 @@
+# default values
diff --git a/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/ec.yaml b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/ec.yaml
new file mode 100644
index 000000000..fa691b67d
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/ec.yaml
@@ -0,0 +1,11 @@
+apiVersion: embeddedcluster.replicated.com/v1beta1
+kind: Config
+metadata:
+  name: ec
+spec:
+  version: 3.0.0
+  extensions:
+    helmCharts:
+      - chart:
+          name: missing-chart
+          chartVersion: 1.0.0
diff --git a/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/helmchart.yaml b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/helmchart.yaml
new file mode 100644
index 000000000..b1b039190
--- /dev/null
+++ b/pkg/lint2/testdata/validation/scenario-8-ec-config-missing-archive/manifests/helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta1
+kind: HelmChart
+metadata:
+  name: other-app
+spec:
+  chart:
+    name: other-app
+    chartVersion: 1.0.0
+  builder: {}
diff --git a/pkg/lint2/validation_integration_test.go b/pkg/lint2/validation_integration_test.go
index 6c59d9485..ee531c414 100644
--- a/pkg/lint2/validation_integration_test.go
+++ b/pkg/lint2/validation_integration_test.go
@@ -374,3 +374,105 @@ func TestLintValidation_AutoDiscovery(t *testing.T) {
 
 	t.Log("Auto-discovery successfully found and validated chart with HelmChart manifest")
 }
+
+// TestLintValidation_ECConfigHelmCharts tests validation with EC Config helmCharts that match a chart.
+func TestLintValidation_ECConfigHelmCharts(t *testing.T) {
+	testDir := filepath.Join("testdata", "validation", "scenario-7-ec-config-helmcharts")
+
+	originalWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(originalWd)
+
+	if err := os.Chdir(testDir); err != nil {
+		t.Fatalf("failed to change to test directory: %v", err)
+	}
+
+	parser := tools.NewConfigParser()
+	config, err := parser.FindAndParseConfig(".")
+	if err != nil {
+		t.Fatalf("failed to load config: %v", err)
+	}
+
+	charts, err := GetChartsWithMetadataFromConfig(config)
+	if err != nil {
+		t.Fatalf("GetChartsWithMetadataFromConfig failed: %v", err)
+	}
+
+	if len(charts) != 1 {
+		t.Fatalf("expected 1 chart, got %d", len(charts))
+	}
+
+	helmCharts, err := DiscoverHelmChartManifests(config.Manifests)
+	if err != nil {
+		t.Fatalf("DiscoverHelmChartManifests failed: %v", err)
+	}
+
+	if len(helmCharts) != 1 {
+		t.Fatalf("expected 1 HelmChart manifest discovered from EC Config, got %d", len(helmCharts))
+	}
+
+	result, err := ValidateChartToHelmChartMapping(charts, helmCharts)
+	if err != nil {
+		t.Fatalf("validation failed: %v", err)
+	}
+
+	if len(result.Warnings) != 0 {
+		t.Errorf("expected no warnings, got %d: %v", len(result.Warnings), result.Warnings)
+	}
+}
+
+// TestLintValidation_ECConfigMissingArchive tests warning when EC Config helmCharts has no matching chart.
+func TestLintValidation_ECConfigMissingArchive(t *testing.T) {
+	testDir := filepath.Join("testdata", "validation", "scenario-8-ec-config-missing-archive")
+
+	originalWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(originalWd)
+
+	if err := os.Chdir(testDir); err != nil {
+		t.Fatalf("failed to change to test directory: %v", err)
+	}
+
+	parser := tools.NewConfigParser()
+	config, err := parser.FindAndParseConfig(".")
+	if err != nil {
+		t.Fatalf("failed to load config: %v", err)
+	}
+
+	charts, err := GetChartsWithMetadataFromConfig(config)
+	if err != nil {
+		t.Fatalf("GetChartsWithMetadataFromConfig failed: %v", err)
+	}
+
+	if len(charts) != 1 {
+		t.Fatalf("expected 1 chart, got %d", len(charts))
+	}
+
+	helmCharts, err := DiscoverHelmChartManifests(config.Manifests)
+	if err != nil {
+		t.Fatalf("DiscoverHelmChartManifests failed: %v", err)
+	}
+
+	if len(helmCharts) != 2 {
+		t.Fatalf("expected 2 manifests (1 kots + 1 EC), got %d", len(helmCharts))
+	}
+
+	result, err := ValidateChartToHelmChartMapping(charts, helmCharts)
+	if err != nil {
+		t.Fatalf("validation failed: %v", err)
+	}
+
+	if len(result.Warnings) != 1 {
+		t.Fatalf("expected 1 warning for orphaned EC Config manifest, got %d: %v", len(result.Warnings), result.Warnings)
+	}
+
+	// Verify the warning mentions the orphaned EC Config chart
+	warning := result.Warnings[0]
+	if !strings.Contains(warning, "missing-chart") {
+		t.Errorf("warning should mention orphaned chart 'missing-chart': %s", warning)
+	}
+}