diff --git a/api/internal/builtins/NamespaceTransformer.go b/api/internal/builtins/NamespaceTransformer.go
index d839fb9751..a96465b9fa 100644
--- a/api/internal/builtins/NamespaceTransformer.go
+++ b/api/internal/builtins/NamespaceTransformer.go
@@ -53,6 +53,12 @@ func (p *NamespaceTransformerPlugin) Transform(m resmap.ResMap) error {
 			// Don't mutate empty objects?
 			continue
 		}
+		if origin, err := r.GetOrigin(); err == nil && origin != nil {
+			if origin.ConfiguredBy.Kind == "HelmChartInflationGenerator" {
+				// Don't apply namespace on Helm generated manifest. Helm should take care of it.
+				continue
+			}
+		}
 		r.StorePreviousId()
 		if err := r.ApplyFilter(namespace.Filter{
 			Namespace:              p.Namespace,
diff --git a/api/internal/target/kusttarget.go b/api/internal/target/kusttarget.go
index 5f1d1095a1..2330e14299 100644
--- a/api/internal/target/kusttarget.go
+++ b/api/internal/target/kusttarget.go
@@ -127,11 +127,11 @@ func (kt *KustTarget) MakeCustomizedResMap() (resmap.ResMap, error) {
 }
 
 func (kt *KustTarget) makeCustomizedResMap() (resmap.ResMap, error) {
-	var origin *resource.Origin
-	if len(kt.kustomization.BuildMetadata) != 0 {
-		origin = &resource.Origin{}
-	}
-	kt.origin = origin
+	// Track origin for all resources so builtins can make decisions
+	// based on where resources originated from.
+	// Origin annotations will be stripped from the output if not
+	// requested via build metadata options.
+	kt.origin = &resource.Origin{}
 	ra, err := kt.AccumulateTarget()
 	if err != nil {
 		return nil, err
@@ -496,6 +496,11 @@ func (kt *KustTarget) accumulateDirectory(
 	}
 	subKt.kustomization.BuildMetadata = kt.kustomization.BuildMetadata
 	subKt.origin = kt.origin
+	// Propagate namespace to child kustomization if child doesn't have one
+	// This ensures Helm charts in base kustomizations inherit namespace from overlays
+	if subKt.kustomization.Namespace == "" && kt.kustomization.Namespace != "" {
+		subKt.kustomization.Namespace = kt.kustomization.Namespace
+	}
 	var bytes []byte
 	if openApiPath, exists := subKt.Kustomization().OpenAPI["path"]; exists {
 		bytes, err = ldr.Load(openApiPath)
diff --git a/api/internal/target/kusttarget_configplugin.go b/api/internal/target/kusttarget_configplugin.go
index 1ba028a36f..0be8488199 100644
--- a/api/internal/target/kusttarget_configplugin.go
+++ b/api/internal/target/kusttarget_configplugin.go
@@ -166,6 +166,11 @@ var generatorConfigurators = map[builtinhelpers.BuiltinPluginType]func(
 		for _, chart := range kt.kustomization.HelmCharts {
 			c.HelmGlobals = globals
 			c.HelmChart = chart
+			// Pass kustomize namespace to helm
+			// Fixes https://github.com/kubernetes-sigs/kustomize/issues/5566
+			if c.HelmChart.Namespace == "" && kt.kustomization.Namespace != "" {
+				c.HelmChart.Namespace = kt.kustomization.Namespace
+			}
 			p := f()
 			if err = kt.configureBuiltinPlugin(p, c, bpt); err != nil {
 				return nil, err
diff --git a/api/internal/target/kusttarget_test.go b/api/internal/target/kusttarget_test.go
index 7993df5acc..beb95f807c 100644
--- a/api/internal/target/kusttarget_test.go
+++ b/api/internal/target/kusttarget_test.go
@@ -300,6 +300,8 @@ metadata:
 		require.NoError(t, expected.Append(r), "failed to append resource: %v")
 	}
 	expected.RemoveBuildAnnotations()
+	require.NoError(t, expected.RemoveTransformerAnnotations())
+	require.NoError(t, expected.RemoveOriginAnnotations())
 	expYaml, err := expected.AsYaml()
 	require.NoError(t, err)
 
@@ -308,6 +310,8 @@ metadata:
 	actual, err := kt.MakeCustomizedResMap()
 	require.NoError(t, err)
 	actual.RemoveBuildAnnotations()
+	require.NoError(t, actual.RemoveTransformerAnnotations())
+	require.NoError(t, actual.RemoveOriginAnnotations())
 	actYaml, err := actual.AsYaml()
 	require.NoError(t, err)
 	assert.Equal(t, string(expYaml), string(actYaml))
@@ -411,6 +415,8 @@ metadata:
 		require.NoError(t, err)
 	}
 	expected.RemoveBuildAnnotations()
+	require.NoError(t, expected.RemoveTransformerAnnotations())
+	require.NoError(t, expected.RemoveOriginAnnotations())
 	expYaml, err := expected.AsYaml()
 	require.NoError(t, err)
 
@@ -419,6 +425,8 @@ metadata:
 	actual, err := kt.MakeCustomizedResMap()
 	require.NoError(t, err)
 	actual.RemoveBuildAnnotations()
+	require.NoError(t, actual.RemoveTransformerAnnotations())
+	require.NoError(t, actual.RemoveOriginAnnotations())
 	actYaml, err := actual.AsYaml()
 	require.NoError(t, err)
 	require.Equal(t, string(expYaml), string(actYaml))
diff --git a/api/krusty/helmchartinflationgenerator_test.go b/api/krusty/helmchartinflationgenerator_test.go
index 7fc3f76e7f..4a0d8bb962 100644
--- a/api/krusty/helmchartinflationgenerator_test.go
+++ b/api/krusty/helmchartinflationgenerator_test.go
@@ -21,10 +21,31 @@ kind: Secret
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
-  name: test-minecraft
+  name: test-minecraft-rcon
+  namespace: default
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-minecraft
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test
+  name: test-minecraft-curseforge
+  namespace: default
 type: Opaque
 ---
 apiVersion: v1
@@ -32,10 +53,14 @@ kind: Service
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft
+  namespace: default
 spec:
   ports:
   - name: minecraft
@@ -150,7 +175,7 @@ func TestHelmChartInflationGeneratorOld(t *testing.T) {
 helmChartInflationGenerator:
 - chartName: minecraft
   chartRepoUrl: https://itzg.github.io/minecraft-server-charts
-  chartVersion: 3.1.3
+  chartVersion: 4.26.4
   releaseName: test
 `)
 
@@ -158,6 +183,54 @@ helmChartInflationGenerator:
 	th.AssertActualEqualsExpected(m, expectedHelm)
 }
 
+func TestHelmChartNamespacePropagation(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarnessWithTmpRoot(t)
+	defer th.Reset()
+	if err := th.ErrIfNoHelm(); err != nil {
+		t.Skip("skipping: " + err.Error())
+	}
+
+	chartDir := filepath.Join(th.GetRoot(), "charts", "service")
+	require.NoError(t, th.GetFSys().MkdirAll(filepath.Join(chartDir, "templates")))
+	th.WriteF(filepath.Join(chartDir, "Chart.yaml"), `
+apiVersion: v2
+name: service
+type: application
+version: 1.0.0
+`)
+	th.WriteF(filepath.Join(chartDir, "values.yaml"), ``)
+	th.WriteF(filepath.Join(chartDir, "templates", "service.yaml"), `
+apiVersion: v1
+kind: Service
+metadata:
+  name: the-bug
+  namespace: {{ .Release.Namespace }}
+  annotations:
+    this-service-is-deployed-in-namespace: {{ .Release.Namespace }}
+`)
+	th.WriteF(filepath.Join(th.GetRoot(), "values.yaml"), ``)
+
+	th.WriteK(th.GetRoot(), `
+helmGlobals:
+  chartHome: ./charts
+namespace: the-actual-namespace
+helmCharts:
+  - name: service
+    releaseName: service
+    valuesFile: values.yaml
+`)
+
+	m := th.Run(th.GetRoot(), th.MakeOptionsPluginsEnabled())
+	th.AssertActualEqualsExpected(m, `apiVersion: v1
+kind: Service
+metadata:
+  annotations:
+    this-service-is-deployed-in-namespace: the-actual-namespace
+  name: the-bug
+  namespace: the-actual-namespace
+`)
+}
+
 func TestHelmChartInflationGenerator(t *testing.T) {
 	th := kusttest_test.MakeEnhancedHarnessWithTmpRoot(t)
 	defer th.Reset()
@@ -169,7 +242,7 @@ func TestHelmChartInflationGenerator(t *testing.T) {
 helmCharts:
 - name: minecraft
   repo: https://itzg.github.io/minecraft-server-charts
-  version: 3.1.3
+  version: 4.26.4
   releaseName: test
 `)
 
@@ -252,7 +325,7 @@ func TestHelmChartProdVsDev(t *testing.T) {
 helmCharts:
 - name: minecraft
   repo: https://itzg.github.io/minecraft-server-charts
-  version: 3.1.3
+  version: 4.26.4
   releaseName: test
 `)
 	th.WriteK(dirProd, `
@@ -287,10 +360,30 @@ kind: Secret
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
-  name: myProd-test-minecraft
+  name: myProd-test-minecraft-rcon
+  namespace: prod
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-minecraft
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test
+  name: myProd-test-minecraft-curseforge
   namespace: prod
 type: Opaque
 ---
@@ -299,7 +392,10 @@ kind: Service
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: myProd-test-minecraft
@@ -325,10 +421,30 @@ kind: Secret
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
-  name: myDev-test-minecraft
+  name: myDev-test-minecraft-rcon
+  namespace: dev
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-minecraft
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test
+  name: myDev-test-minecraft-curseforge
   namespace: dev
 type: Opaque
 ---
@@ -337,7 +453,10 @@ kind: Service
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: myDev-test-minecraft
@@ -359,10 +478,30 @@ kind: Secret
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
-  name: myProd-test-minecraft
+  name: myProd-test-minecraft-rcon
+  namespace: prod
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-minecraft
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test
+  name: myProd-test-minecraft-curseforge
   namespace: prod
 type: Opaque
 ---
@@ -371,7 +510,10 @@ kind: Service
 metadata:
   labels:
     app: test-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: myProd-test-minecraft
@@ -586,11 +728,11 @@ helmCharts:
     skipTests: true
   - name: minecraft
     repo: https://itzg.github.io/minecraft-server-charts
-    version: 3.1.3
+    version: 4.26.4
     releaseName: test-1
   - name: minecraft
     repo: https://itzg.github.io/minecraft-server-charts
-    version: 3.1.4
+    version: 4.26.4
     releaseName: test-2
 `)
 
@@ -621,10 +763,30 @@ kind: Secret
 metadata:
   labels:
     app: test-1-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-1-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test-1
-  name: test-1-minecraft
+  name: test-1-minecraft-rcon
+  namespace: default
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-1-minecraft
+    app.kubernetes.io/instance: test-1-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test-1
+  name: test-1-minecraft-curseforge
   namespace: default
 type: Opaque
 ---
@@ -633,7 +795,10 @@ kind: Service
 metadata:
   labels:
     app: test-1-minecraft
-    chart: minecraft-3.1.3
+    app.kubernetes.io/instance: test-1-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test-1
   name: test-1-minecraft
@@ -655,10 +820,30 @@ kind: Secret
 metadata:
   labels:
     app: test-2-minecraft
-    chart: minecraft-3.1.4
+    app.kubernetes.io/instance: test-2-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test-2
-  name: test-2-minecraft
+  name: test-2-minecraft-rcon
+  namespace: default
+type: Opaque
+---
+apiVersion: v1
+data:
+  cf-api-key: Q0hBTkdFTUUh
+kind: Secret
+metadata:
+  labels:
+    app: test-2-minecraft
+    app.kubernetes.io/instance: test-2-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
+    heritage: Helm
+    release: test-2
+  name: test-2-minecraft-curseforge
   namespace: default
 type: Opaque
 ---
@@ -667,7 +852,10 @@ kind: Service
 metadata:
   labels:
     app: test-2-minecraft
-    chart: minecraft-3.1.4
+    app.kubernetes.io/instance: test-2-minecraft
+    app.kubernetes.io/name: minecraft
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test-2
   name: test-2-minecraft
@@ -698,7 +886,7 @@ namespace: default
 helmCharts:
   - name: minecraft
     repo: https://itzg.github.io/minecraft-server-charts
-    version: 4.11.0
+    version: 4.26.4
     releaseName: test
     kubeVersion: "1.16"
     valuesInline:
@@ -724,8 +912,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-rcon
@@ -741,8 +929,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-curseforge
@@ -756,8 +944,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft
@@ -779,8 +967,8 @@ metadata:
     app: test-minecraft-map
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-map
@@ -794,7 +982,7 @@ namespace: default
 helmCharts:
   - name: minecraft
     repo: https://itzg.github.io/minecraft-server-charts
-    version: 4.11.0
+    version: 4.26.4
     releaseName: test
     kubeVersion: "1.27"
     valuesInline:
@@ -820,8 +1008,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-rcon
@@ -837,8 +1025,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-curseforge
@@ -852,8 +1040,8 @@ metadata:
     app: test-minecraft
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft
@@ -875,8 +1063,8 @@ metadata:
     app: test-minecraft-map
     app.kubernetes.io/instance: test-minecraft
     app.kubernetes.io/name: minecraft
-    app.kubernetes.io/version: 4.11.0
-    chart: minecraft-4.11.0
+    app.kubernetes.io/version: 4.26.4
+    chart: minecraft-4.26.4
     heritage: Helm
     release: test
   name: test-minecraft-map
@@ -886,6 +1074,159 @@ spec:
 `)
 }
 
+func TestHelmChartNamespacePropagationViaResources(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarnessWithTmpRoot(t)
+	defer th.Reset()
+	if err := th.ErrIfNoHelm(); err != nil {
+		t.Skip("skipping: " + err.Error())
+	}
+
+	// Create base directory with helm chart
+	baseDir := th.MkDir("base")
+	chartDir := filepath.Join(baseDir, "charts", "service")
+	require.NoError(t, th.GetFSys().MkdirAll(filepath.Join(chartDir, "templates")))
+	th.WriteF(filepath.Join(chartDir, "Chart.yaml"), `
+apiVersion: v2
+name: service
+type: application
+version: 1.0.0
+`)
+	th.WriteF(filepath.Join(chartDir, "values.yaml"), ``)
+	th.WriteF(filepath.Join(chartDir, "templates", "service.yaml"), `
+apiVersion: v1
+kind: Service
+metadata:
+  name: test-service
+  namespace: {{ .Release.Namespace }}
+  annotations:
+    deployed-in-namespace: {{ .Release.Namespace }}
+`)
+
+	// Base kustomization with helmCharts
+	th.WriteK(baseDir, `
+helmGlobals:
+  chartHome: ./charts
+helmCharts:
+  - name: service
+    releaseName: service
+`)
+
+	// Overlay that references base via resources and sets namespace
+	overlayDir := th.MkDir("overlay")
+	th.WriteK(overlayDir, `
+namespace: production
+resources:
+  - ../base
+`)
+
+	m := th.Run(overlayDir, th.MakeOptionsPluginsEnabled())
+	th.AssertActualEqualsExpected(m, `apiVersion: v1
+kind: Service
+metadata:
+  annotations:
+    deployed-in-namespace: production
+  name: test-service
+  namespace: production
+`)
+}
+
+func TestHelmChartDifferentNamespaces(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarnessWithTmpRoot(t)
+	defer th.Reset()
+	if err := th.ErrIfNoHelm(); err != nil {
+		t.Skip("skipping: " + err.Error())
+	}
+
+	chartDir := filepath.Join(th.GetRoot(), "charts", "service")
+	require.NoError(t, th.GetFSys().MkdirAll(filepath.Join(chartDir, "templates")))
+	th.WriteF(filepath.Join(chartDir, "Chart.yaml"), `
+apiVersion: v2
+name: service
+type: application
+version: 1.0.0
+`)
+	th.WriteF(filepath.Join(chartDir, "values.yaml"), ``)
+	th.WriteF(filepath.Join(chartDir, "templates", "service.yaml"), `
+apiVersion: v1
+kind: Service
+metadata:
+  name: test-service
+  namespace: {{ .Release.Namespace }}
+  annotations:
+    helm-namespace: {{ .Release.Namespace }}
+`)
+
+	// Test with different namespaces in transformer vs helmCharts.namespace
+	th.WriteK(th.GetRoot(), `
+helmGlobals:
+  chartHome: ./charts
+namespace: transformer-ns
+helmCharts:
+  - name: service
+    releaseName: service
+    namespace: helm-ns
+`)
+
+	m := th.Run(th.GetRoot(), th.MakeOptionsPluginsEnabled())
+	// helmCharts.namespace should take precedence
+	th.AssertActualEqualsExpected(m, `apiVersion: v1
+kind: Service
+metadata:
+  annotations:
+    helm-namespace: helm-ns
+  name: test-service
+  namespace: helm-ns
+`)
+}
+
+func TestHelmChartSameNamespace(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarnessWithTmpRoot(t)
+	defer th.Reset()
+	if err := th.ErrIfNoHelm(); err != nil {
+		t.Skip("skipping: " + err.Error())
+	}
+
+	chartDir := filepath.Join(th.GetRoot(), "charts", "service")
+	require.NoError(t, th.GetFSys().MkdirAll(filepath.Join(chartDir, "templates")))
+	th.WriteF(filepath.Join(chartDir, "Chart.yaml"), `
+apiVersion: v2
+name: service
+type: application
+version: 1.0.0
+`)
+	th.WriteF(filepath.Join(chartDir, "values.yaml"), ``)
+	th.WriteF(filepath.Join(chartDir, "templates", "service.yaml"), `
+apiVersion: v1
+kind: Service
+metadata:
+  name: test-service
+  namespace: {{ .Release.Namespace }}
+  annotations:
+    deployed-namespace: {{ .Release.Namespace }}
+`)
+
+	// Test with same namespace in both places
+	th.WriteK(th.GetRoot(), `
+helmGlobals:
+  chartHome: ./charts
+namespace: shared-namespace
+helmCharts:
+  - name: service
+    releaseName: service
+    namespace: shared-namespace
+`)
+
+	m := th.Run(th.GetRoot(), th.MakeOptionsPluginsEnabled())
+	th.AssertActualEqualsExpected(m, `apiVersion: v1
+kind: Service
+metadata:
+  annotations:
+    deployed-namespace: shared-namespace
+  name: test-service
+  namespace: shared-namespace
+`)
+}
+
 func copyValuesFilesTestChartsIntoHarness(t *testing.T, th *kusttest_test.HarnessEnhanced) {
 	t.Helper()
 
diff --git a/plugin/builtin/namespacetransformer/NamespaceTransformer.go b/plugin/builtin/namespacetransformer/NamespaceTransformer.go
index 9b395ef9fb..43256d106d 100644
--- a/plugin/builtin/namespacetransformer/NamespaceTransformer.go
+++ b/plugin/builtin/namespacetransformer/NamespaceTransformer.go
@@ -56,6 +56,12 @@ func (p *plugin) Transform(m resmap.ResMap) error {
 			// Don't mutate empty objects?
 			continue
 		}
+		if origin, err := r.GetOrigin(); err == nil && origin != nil {
+			if origin.ConfiguredBy.Kind == "HelmChartInflationGenerator" {
+				// Don't apply namespace on Helm generated manifest. Helm should take care of it.
+				continue
+			}
+		}
 		r.StorePreviousId()
 		if err := r.ApplyFilter(namespace.Filter{
 			Namespace:              p.Namespace,
diff --git a/plugin/builtin/namespacetransformer/NamespaceTransformer_test.go b/plugin/builtin/namespacetransformer/NamespaceTransformer_test.go
index 6fc510c134..660e46d038 100644
--- a/plugin/builtin/namespacetransformer/NamespaceTransformer_test.go
+++ b/plugin/builtin/namespacetransformer/NamespaceTransformer_test.go
@@ -8,7 +8,12 @@ import (
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"sigs.k8s.io/kustomize/api/provider"
+	"sigs.k8s.io/kustomize/api/resmap"
+	"sigs.k8s.io/kustomize/api/resource"
 	kusttest_test "sigs.k8s.io/kustomize/api/testutils/kusttest"
+	kyaml "sigs.k8s.io/kustomize/kyaml/yaml"
 )
 
 const defaultFieldSpecs = `
@@ -762,3 +767,41 @@ subjects:
 `)
 		})
 }
+
+func TestNamespaceTransformer_SkipHelmOrigin(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("NamespaceTransformer")
+	defer th.Reset()
+
+	rmF := resmap.NewFactory(provider.NewDefaultDepProvider().GetResourceFactory())
+	rm, err := rmF.NewResMapFromBytes([]byte(`apiVersion: v1
+kind: Service
+metadata:
+  name: svc
+  namespace: helm-ns
+`))
+	require.NoError(t, err)
+	r := rm.Resources()[0]
+	origin := &resource.Origin{
+		ConfiguredBy: kyaml.ResourceIdentifier{
+			TypeMeta: kyaml.TypeMeta{APIVersion: "builtin", Kind: "HelmChartInflationGenerator"},
+		},
+	}
+	require.NoError(t, r.SetOrigin(origin))
+
+	rm, err = th.RunTransformerFromResMap(`
+apiVersion: builtin
+kind: NamespaceTransformer
+metadata:
+  name: notImportantHere
+  namespace: test
+`+defaultFieldSpecs, rm)
+	require.NoError(t, err)
+	require.NoError(t, rm.RemoveOriginAnnotations())
+	th.AssertActualEqualsExpectedNoIdAnnotations(rm, `apiVersion: v1
+kind: Service
+metadata:
+  name: svc
+  namespace: helm-ns
+`)
+}