diff --git a/flytestdlib/config/tests/accessor_test.go b/flytestdlib/config/tests/accessor_test.go
index 899938be644..842dac9afe7 100644
--- a/flytestdlib/config/tests/accessor_test.go
+++ b/flytestdlib/config/tests/accessor_test.go
@@ -89,6 +89,16 @@ type ComplexType struct {
 
 type ComplexTypeArray []ComplexType
 
+type Plugin struct {
+	Name        string            `json:"name"`
+	Annotations map[string]string `json:"annotations"`
+}
+
+type DottedKeysConfig struct {
+	Annotations map[string]string `json:"annotations"`
+	Plugins     []Plugin          `json:"plugins"`
+}
+
 type ConfigWithLists struct {
 	ListOfStuff []ComplexType `json:"list"`
 	StringValue string        `json:"string-val"`
@@ -403,6 +413,27 @@ func TestAccessor_UpdateConfig(t *testing.T) {
 				assert.Equal(t, "xyz1", r.ItemsMap["itemA"]["itemAb"].ID)
 				assert.Equal(t, "xyz2", r.ItemsMap["itemB"]["itemBb"].ID)
 			})
+
+			t.Run("DottedKeysEndToEnd", func(t *testing.T) {
+				root := config.NewRootSection()
+				_, err := root.RegisterSection("dotted-keys", &DottedKeysConfig{})
+				assert.NoError(t, err)
+
+				v := provider(config.Options{
+					SearchPaths: []string{filepath.Join("testdata", "dotted_keys_config.yaml")},
+					RootSection: root,
+				})
+
+				assert.NoError(t, v.UpdateConfig(context.TODO()))
+				r := root.GetSection("dotted-keys").GetConfig().(*DottedKeysConfig)
+
+				assert.Equal(t, "false", r.Annotations["cluster-autoscaler.kubernetes.io/safe-to-evict"])
+				assert.Equal(t, "true", r.Annotations["sidecar.istio.io/inject"])
+
+				assert.Len(t, r.Plugins, 1)
+				assert.Equal(t, "KeepMyCase", r.Plugins[0].Name)
+				assert.Equal(t, "/etc/plugin", r.Plugins[0].Annotations["config.path"])
+			})
 		})
 
 		t.Run(fmt.Sprintf("[%v] Override in Env Var", provider(config.Options{}).ID()), func(t *testing.T) {
diff --git a/flytestdlib/config/tests/testdata/dotted_keys_config.yaml b/flytestdlib/config/tests/testdata/dotted_keys_config.yaml
new file mode 100644
index 00000000000..d2ffeee831f
--- /dev/null
+++ b/flytestdlib/config/tests/testdata/dotted_keys_config.yaml
@@ -0,0 +1,8 @@
+dotted-keys:
+  annotations:
+    cluster-autoscaler.kubernetes.io/safe-to-evict: "false"
+    sidecar.istio.io/inject: "true"
+  plugins:
+    - name: KeepMyCase
+      annotations:
+        config.path: /etc/plugin
diff --git a/flytestdlib/config/viper/viper.go b/flytestdlib/config/viper/viper.go
index ad3c461860b..8440776b8ae 100644
--- a/flytestdlib/config/viper/viper.go
+++ b/flytestdlib/config/viper/viper.go
@@ -289,6 +289,7 @@ func (v viperAccessor) parseViperConfig(root config.Section) error {
 		}
 
 		restoreCaseSensitiveArrayKeys(settings, rawSettings)
+		restoreDottedMapKeys(settings, rawSettings)
 	}
 
 	return v.parseViperConfigRecursive(root, settings)
@@ -324,6 +325,84 @@ func restoreCaseSensitiveArrayKeys(viperData, rawData map[string]interface{}) {
 	}
 }
 
+// restoreDottedMapKeys undoes viper's splitting of dotted YAML keys.
+//
+//   - Viper hard-codes "." as its key delimiter and splits every key on it,
+//     so a YAML leaf key like "test.annotation" arrives in viperData as the
+//     nested map {"test": {"annotation": ...}}.
+//   - rawData is the authoritative source for what the user wrote.
+//   - We walk rawData, detect dotted keys, drop the nested skeleton from
+//     viperData, and reinsert the value under its original dotted key.
+func restoreDottedMapKeys(viperData, rawData map[string]interface{}) {
+	for rawKey, rawVal := range rawData {
+		if strings.Contains(rawKey, keyDelim) {
+			// Drop the nested skeleton viper built from this dotted key, then
+			// reinsert the raw value under the original key. Lowercase the
+			// path because viper lowercases all keys.
+			pruneSplitPath(viperData, strings.Split(strings.ToLower(rawKey), keyDelim))
+			viperData[rawKey] = rawVal
+			continue
+		}
+
+		// rawVal may itself be a map containing dotted keys deeper down
+		// (e.g. annotations: {test.annotation: ...}); recurse to fix them.
+		viperKey, ok := findViperKey(viperData, rawKey)
+		if !ok {
+			continue
+		}
+		if rawMap, ok := rawVal.(map[string]interface{}); ok {
+			if viperMap, ok := viperData[viperKey].(map[string]interface{}); ok {
+				restoreDottedMapKeys(viperMap, rawMap)
+			}
+		}
+	}
+}
+
+// findViperKey returns the key in viperData that case-insensitively matches
+// rawKey. Viper lowercases all keys internally, but raw YAML preserves the
+// original casing, so we must scan.
+func findViperKey(viperData map[string]interface{}, rawKey string) (string, bool) {
+	for k := range viperData {
+		if strings.EqualFold(k, rawKey) {
+			return k, true
+		}
+	}
+	return "", false
+}
+
+// pruneSplitPath removes the nested-map skeleton viper created when it split a
+// dotted key on ".". It walks the path top-down, deleting only nodes that
+// have no remaining children, so sibling keys that share a prefix are left
+// intact (e.g. removing "a.b.c" must not drop "a.b.d").
+func pruneSplitPath(m map[string]interface{}, parts []string) {
+	if len(parts) == 0 {
+		return
+	}
+	head := parts[0]
+	child, ok := m[head]
+	if !ok {
+		// head not in the map m, directly return.
+		return
+	}
+	if len(parts) == 1 {
+		// Leaf of the split path — this is the value viper produced from the
+		// dotted key. Drop it; the caller will reinsert the raw value.
+		delete(m, head)
+		return
+	}
+	childMap, ok := child.(map[string]interface{})
+	if !ok {
+		// Path diverges from what viper would have produced; leave alone.
+		return
+	}
+	pruneSplitPath(childMap, parts[1:])
+	// Drop the parent if recursion emptied it — keeps the cleanup tight so we
+	// don't leave behind empty intermediate maps from the split.
+	if len(childMap) == 0 {
+		delete(m, head)
+	}
+}
+
 func (v viperAccessor) parseViperConfigRecursive(root config.Section, settings interface{}) error {
 	errs := stdLibErrs.ErrorCollection{}
 	var mine interface{}
diff --git a/flytestdlib/config/viper/viper_test.go b/flytestdlib/config/viper/viper_test.go
index 881d4436f2c..ecbbbacd1f7 100644
--- a/flytestdlib/config/viper/viper_test.go
+++ b/flytestdlib/config/viper/viper_test.go
@@ -52,3 +52,171 @@ func Test_stringToByteArray(t *testing.T) {
 		assert.NotEqual(t, []byte("hello"), res)
 	})
 }
+
+func Test_restoreDottedMapKeys(t *testing.T) {
+	t.Run("siblings sharing dotted prefix", func(t *testing.T) {
+		viper := map[string]interface{}{
+			"annotations": map[string]interface{}{
+				"test": map[string]interface{}{
+					"annotation": "true",
+					"other":      "false",
+				},
+			},
+		}
+		raw := map[string]interface{}{
+			"annotations": map[string]interface{}{
+				"test.annotation": "true",
+				"test.other":      "false",
+			},
+		}
+
+		restoreDottedMapKeys(viper, raw)
+
+		assert.Equal(t, map[string]interface{}{
+			"annotations": map[string]interface{}{
+				"test.annotation": "true",
+				"test.other":      "false",
+			},
+		}, viper)
+	})
+
+	t.Run("case-insensitive recursion into nested map", func(t *testing.T) {
+		viper := map[string]interface{}{
+			"annotations": map[string]interface{}{
+				"test": map[string]interface{}{"annotation": "true"},
+			},
+		}
+		raw := map[string]interface{}{
+			"Annotations": map[string]interface{}{
+				"test.annotation": "true",
+			},
+		}
+
+		restoreDottedMapKeys(viper, raw)
+
+		assert.Equal(t, map[string]interface{}{
+			"annotations": map[string]interface{}{
+				"test.annotation": "true",
+			},
+		}, viper)
+	})
+
+	t.Run("dotted key with map value", func(t *testing.T) {
+		viper := map[string]interface{}{
+			"a": map[string]interface{}{
+				"b": map[string]interface{}{
+					"c": map[string]interface{}{"d": "v"},
+				},
+			},
+		}
+		raw := map[string]interface{}{
+			"a.b": map[string]interface{}{
+				"c.d": "v",
+			},
+		}
+
+		restoreDottedMapKeys(viper, raw)
+
+		assert.Equal(t, map[string]interface{}{
+			"a.b": map[string]interface{}{
+				"c.d": "v",
+			},
+		}, viper)
+	})
+
+	t.Run("dotted and non-dotted siblings at top level", func(t *testing.T) {
+		viper := map[string]interface{}{
+			"a": map[string]interface{}{
+				"b": "from-dotted",
+				"x": "from-non-dotted",
+			},
+		}
+		raw := map[string]interface{}{
+			"a.b": "from-dotted",
+			"a":   map[string]interface{}{"x": "from-non-dotted"},
+		}
+
+		restoreDottedMapKeys(viper, raw)
+
+		assert.Equal(t, map[string]interface{}{
+			"a.b": "from-dotted",
+			"a":   map[string]interface{}{"x": "from-non-dotted"},
+		}, viper)
+	})
+
+	// This test case covers the usecases mentioned in issue #6166
+	t.Run("k8s annotation key", func(t *testing.T) {
+		viper := map[string]interface{}{
+			"default-annotations": map[string]interface{}{
+				"cluster-autoscaler": map[string]interface{}{
+					"kubernetes": map[string]interface{}{
+						"io/safe-to-evict": "false",
+					},
+				},
+			},
+		}
+		raw := map[string]interface{}{
+			"default-annotations": map[string]interface{}{
+				"cluster-autoscaler.kubernetes.io/safe-to-evict": "false",
+			},
+		}
+
+		restoreDottedMapKeys(viper, raw)
+
+		assert.Equal(t, map[string]interface{}{
+			"default-annotations": map[string]interface{}{
+				"cluster-autoscaler.kubernetes.io/safe-to-evict": "false",
+			},
+		}, viper)
+	})
+}
+
+func Test_pruneSplitPath(t *testing.T) {
+	t.Run("preserves sibling under shared prefix", func(t *testing.T) {
+		m := map[string]interface{}{
+			"test": map[string]interface{}{
+				"annotation": "v1",
+				"other":      "v2",
+			},
+		}
+
+		pruneSplitPath(m, []string{"test", "annotation"})
+
+		assert.Equal(t, map[string]interface{}{
+			"test": map[string]interface{}{"other": "v2"},
+		}, m)
+	})
+
+	t.Run("collapses entire chain when emptied", func(t *testing.T) {
+		m := map[string]interface{}{
+			"a": map[string]interface{}{
+				"b": map[string]interface{}{"c": "v"},
+			},
+		}
+
+		pruneSplitPath(m, []string{"a", "b", "c"})
+
+		assert.Equal(t, map[string]interface{}{}, m)
+	})
+
+	t.Run("path diverges from viper structure", func(t *testing.T) {
+		m := map[string]interface{}{"a": "scalar"}
+
+		pruneSplitPath(m, []string{"a", "b"})
+
+		assert.Equal(t, map[string]interface{}{"a": "scalar"}, m)
+	})
+}
+
+func Test_findViperKey(t *testing.T) {
+	t.Run("case-insensitive match", func(t *testing.T) {
+		k, ok := findViperKey(map[string]interface{}{"foo": 1}, "Foo")
+		assert.True(t, ok)
+		assert.Equal(t, "foo", k)
+	})
+
+	t.Run("not found", func(t *testing.T) {
+		_, ok := findViperKey(map[string]interface{}{"foo": 1}, "bar")
+		assert.False(t, ok)
+	})
+}