diff --git a/api/krusty/generatormergeandreplace_test.go b/api/krusty/generatormergeandreplace_test.go
index 0dff5ae9b..677bfb260 100644
--- a/api/krusty/generatormergeandreplace_test.go
+++ b/api/krusty/generatormergeandreplace_test.go
@@ -453,6 +453,42 @@ metadata:
 `)
 }
 
+// Regression test for https://github.com/kubernetes-sigs/kustomize/issues/5955
+func TestSecretGeneratorMergeStringData(t *testing.T) {
+	th := kusttest_test.MakeHarness(t)
+	th.WriteK(".", `
+resources:
+- secret.yaml
+secretGenerator:
+- name: test
+  behavior: merge
+  literals:
+  - property2=value2
+  options:
+    disableNameSuffixHash: false
+`)
+	th.WriteF("secret.yaml", `
+apiVersion: v1
+kind: Secret
+metadata:
+  name: test
+type: Opaque
+stringData:
+  property1: value1
+`)
+	m := th.Run(".", th.MakeDefaultOptions())
+	th.AssertActualEqualsExpected(m, `
+apiVersion: v1
+data:
+  property1: dmFsdWUx
+  property2: dmFsdWUy
+kind: Secret
+metadata:
+  name: test
+type: Opaque
+`)
+}
+
 func TestMergeAndReplaceDisableNameSuffixHashGenerators(t *testing.T) {
 	th := kusttest_test.MakeHarness(t)
 	th.WriteK("app", `
diff --git a/api/resmap/reswrangler.go b/api/resmap/reswrangler.go
index 33578a0bb..4883cac49 100644
--- a/api/resmap/reswrangler.go
+++ b/api/resmap/reswrangler.go
@@ -588,8 +588,15 @@ func (m *resWrangler) appendReplaceOrMerge(res *resource.Resource) error {
 			if err != nil {
 				return err
 			}
+			oldForData := old
+			if res.GetApiVersion() == "v1" && res.GetKind() == "Secret" {
+				oldForData, err = normalizeSecretStringData(old)
+				if err != nil {
+					return fmt.Errorf("failed to normalize stringData for %s: %w", id, err)
+				}
+			}
 			res.CopyMergeMetaDataFieldsFrom(old)
-			res.MergeDataMapFrom(old)
+			res.MergeDataMapFrom(oldForData)
 			res.MergeBinaryDataMapFrom(old)
 			if orig != nil {
 				res.SetOrigin(orig)
@@ -614,6 +621,38 @@ func (m *resWrangler) appendReplaceOrMerge(res *resource.Resource) error {
 	}
 }
 
+// normalizeSecretStringData returns a copy of res with stringData encoded into
+// data, matching the normalization performed by the Kubernetes API server.
+// Values in stringData take precedence over values with the same key in data.
+func normalizeSecretStringData(res *resource.Resource) (*resource.Resource, error) {
+	normalized := res.DeepCopy()
+	stringData, err := normalized.Pipe(kyaml.Lookup("stringData"))
+	if err != nil {
+		return nil, fmt.Errorf("lookup stringData: %w", err)
+	}
+	if !kyaml.IsMissingOrNull(stringData) {
+		values := map[string]string{}
+		if err := stringData.VisitFields(func(node *kyaml.MapNode) error {
+			key := kyaml.GetValue(node.Key)
+			value := node.Value
+			if value == nil || value.YNode() == nil || value.YNode().Kind != kyaml.ScalarNode {
+				return fmt.Errorf("stringData value for key %q must be a scalar", key)
+			}
+			values[key] = kyaml.GetValue(value)
+			return nil
+		}); err != nil {
+			return nil, fmt.Errorf("read stringData: %w", err)
+		}
+		if err := normalized.LoadMapIntoSecretData(values); err != nil {
+			return nil, fmt.Errorf("encode stringData: %w", err)
+		}
+	}
+	if err := normalized.PipeE(kyaml.Clear("stringData")); err != nil {
+		return nil, fmt.Errorf("clear stringData: %w", err)
+	}
+	return normalized, nil
+}
+
 // AnnotateAll implements ResMap
 func (m *resWrangler) AnnotateAll(key string, value string) error {
 	return m.ApplyFilter(annotations.Filter{
diff --git a/api/resmap/reswrangler_test.go b/api/resmap/reswrangler_test.go
index 73c7d7142..59df4f60f 100644
--- a/api/resmap/reswrangler_test.go
+++ b/api/resmap/reswrangler_test.go
@@ -990,6 +990,144 @@ func TestAbsorbAll(t *testing.T) {
 		t, strings.Contains(err.Error(), "behavior must be merge or replace"))
 }
 
+func TestAbsorbAllMergeSecretStringData(t *testing.T) {
+	tests := []struct {
+		name     string
+		existing string
+		incoming string
+		expected string
+	}{
+		{
+			name: "core v1 Secret normalizes stringData",
+			existing: `
+apiVersion: v1
+data:
+  dataOnly: ZGF0YQ==
+  generatorWins: b2xkLWRhdGE=
+  stringWins: b2xkLWRhdGE=
+kind: Secret
+metadata:
+  name: test
+stringData:
+  generatorWins: string
+  long: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
+  multiline: |
+    line one
+    line two
+  stringOnly: string
+  stringWins: string
+type: Opaque
+`,
+			incoming: `
+apiVersion: v1
+data:
+  generatedOnly: Z2VuZXJhdGVk
+  generatorWins: Z2VuZXJhdGVk
+kind: Secret
+metadata:
+  name: test
+type: Opaque
+`,
+			expected: `
+apiVersion: v1
+data:
+  dataOnly: ZGF0YQ==
+  generatedOnly: Z2VuZXJhdGVk
+  generatorWins: Z2VuZXJhdGVk
+  long: |
+    YWJjZGVmZ2hpamtsbW5vcHFyc3R1dnd4eXpBQkNERUZHSElKS0xNTk9QUVJTVFVWV1hZWj
+    AxMjM0NTY3ODk=
+  multiline: bGluZSBvbmUKbGluZSB0d28K
+  stringOnly: c3RyaW5n
+  stringWins: c3RyaW5n
+kind: Secret
+metadata:
+  name: test
+type: Opaque
+`,
+		},
+		{
+			name: "custom resource does not normalize stringData",
+			existing: `
+apiVersion: example.com/v1
+data:
+  oldOnly: b2xk
+kind: Secret
+metadata:
+  name: test
+stringData:
+  customOnly: plain
+`,
+			incoming: `
+apiVersion: example.com/v1
+data:
+  generatedOnly: Z2VuZXJhdGVk
+kind: Secret
+metadata:
+  name: test
+`,
+			expected: `
+apiVersion: example.com/v1
+data:
+  generatedOnly: Z2VuZXJhdGVk
+  oldOnly: b2xk
+kind: Secret
+metadata:
+  name: test
+`,
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			existing, err := rmF.NewResMapFromBytes([]byte(tc.existing))
+			require.NoError(t, err)
+			incoming, err := rmF.NewResMapFromBytes([]byte(tc.incoming))
+			require.NoError(t, err)
+			incoming.Resources()[0].SetBehavior(types.BehaviorMerge)
+			expected, err := rmF.NewResMapFromBytes([]byte(tc.expected))
+			require.NoError(t, err)
+
+			require.NoError(t, existing.AbsorbAll(incoming))
+			existing.RemoveBuildAnnotations()
+			require.NoError(t, expected.ErrorIfNotEqualLists(existing))
+		})
+	}
+}
+
+func TestAbsorbAllRejectsNonScalarSecretStringData(t *testing.T) {
+	existing, err := rmF.NewResMapFromBytes([]byte(`
+apiVersion: v1
+kind: Secret
+metadata:
+  name: test
+stringData:
+  invalid:
+    nested: value
+type: Opaque
+`))
+	require.NoError(t, err)
+	incoming, err := rmF.NewResMapFromBytes([]byte(`
+apiVersion: v1
+data:
+  generated: Z2VuZXJhdGVk
+kind: Secret
+metadata:
+  name: test
+type: Opaque
+`))
+	require.NoError(t, err)
+	incoming.Resources()[0].SetBehavior(types.BehaviorMerge)
+	before, err := existing.AsYaml()
+	require.NoError(t, err)
+
+	err = existing.AbsorbAll(incoming)
+	require.ErrorContains(t, err, `stringData value for key "invalid" must be a scalar`)
+	after, yamlErr := existing.AsYaml()
+	require.NoError(t, yamlErr)
+	assert.Equal(t, before, after)
+}
+
 func TestToRNodeSlice(t *testing.T) {
 	input := `apiVersion: rbac.authorization.k8s.io/v1
 kind: ClusterRole