diff --git a/internal/builder/dynamic_mappings.go b/internal/builder/dynamic_mappings.go
index da0026e50..beeb9a978 100644
--- a/internal/builder/dynamic_mappings.go
+++ b/internal/builder/dynamic_mappings.go
@@ -240,7 +240,7 @@ func formatResult(result interface{}) ([]byte, error) {
 	if err != nil {
 		return nil, errors.New("failed to encode")
 	}
-	yamlFormatter := &formatter.YAMLFormatter{}
+	yamlFormatter := formatter.NewYAMLFormatter(formatter.KeysWithDotActionNone)
 	d, _, err = yamlFormatter.Format(d)
 	if err != nil {
 		return nil, errors.New("failed to format")
diff --git a/internal/formatter/formatter.go b/internal/formatter/formatter.go
index ed16e8658..97367abac 100644
--- a/internal/formatter/formatter.go
+++ b/internal/formatter/formatter.go
@@ -14,14 +14,27 @@ import (
 	"github.com/elastic/elastic-package/internal/packages"
 )
 
+const (
+	KeysWithDotActionNone int = iota
+	KeysWithDotActionNested
+)
+
+type formatterOptions struct {
+	extension                 string
+	specVersion               semver.Version
+	preferedKeysWithDotAction int
+
+	failFast bool
+}
+
 type formatter func(content []byte) ([]byte, bool, error)
 
-func newFormatter(specVersion semver.Version, ext string) formatter {
-	switch ext {
+func newFormatter(options formatterOptions) formatter {
+	switch options.extension {
 	case ".json":
-		return JSONFormatterBuilder(specVersion).Format
+		return JSONFormatterBuilder(options.specVersion).Format
 	case ".yaml", ".yml":
-		return NewYAMLFormatter(specVersion).Format
+		return NewYAMLFormatter(options.preferedKeysWithDotAction).Format
 	default:
 		return nil
 	}
@@ -37,18 +50,33 @@ func Format(packageRoot string, failFast bool) error {
 	if err != nil {
 		return fmt.Errorf("failed to parse package format version %q: %w", manifest.SpecVersion, err)
 	}
+
 	err = filepath.Walk(packageRoot, func(path string, info os.FileInfo, err error) error {
 		if err != nil {
 			return err
 		}
 
+		options := formatterOptions{
+			specVersion: *specVersion,
+			extension:   filepath.Ext(info.Name()),
+			failFast:    failFast,
+		}
+
 		if info.IsDir() && info.Name() == "ingest_pipeline" {
 			return filepath.SkipDir
 		}
 		if info.IsDir() {
 			return nil
 		}
-		err = formatFile(path, failFast, *specVersion)
+
+		// Configure handling of keys with dots.
+		if !specVersion.LessThan(semver.MustParse("3.0.0")) {
+			if info.Name() == "manifest.yml" {
+				options.preferedKeysWithDotAction = KeysWithDotActionNested
+			}
+		}
+
+		err = formatFile(path, options)
 		if err != nil {
 			return fmt.Errorf("formatting file failed (path: %s): %w", path, err)
 		}
@@ -61,14 +89,13 @@ func Format(packageRoot string, failFast bool) error {
 	return nil
 }
 
-func formatFile(path string, failFast bool, specVersion semver.Version) error {
+func formatFile(path string, options formatterOptions) error {
 	content, err := os.ReadFile(path)
 	if err != nil {
 		return fmt.Errorf("reading file content failed: %w", err)
 	}
 
-	ext := filepath.Ext(filepath.Base(path))
-	format := newFormatter(specVersion, ext)
+	format := newFormatter(options)
 	if format == nil {
 		return nil // no errors returned as we have few files that will be never formatted (png, svg, log, etc.)
 	}
@@ -82,7 +109,7 @@ func formatFile(path string, failFast bool, specVersion semver.Version) error {
 		return nil
 	}
 
-	if failFast {
+	if options.failFast {
 		return fmt.Errorf("file is not formatted (path: %s)", path)
 	}
 
diff --git a/internal/formatter/yaml_formatter.go b/internal/formatter/yaml_formatter.go
index 28e3d8ab2..1ab5aebd5 100644
--- a/internal/formatter/yaml_formatter.go
+++ b/internal/formatter/yaml_formatter.go
@@ -9,18 +9,17 @@ import (
 	"fmt"
 	"strings"
 
-	"github.com/Masterminds/semver/v3"
 	"gopkg.in/yaml.v3"
 )
 
 // YAMLFormatter is responsible for formatting the given YAML input.
 type YAMLFormatter struct {
-	specVersion semver.Version
+	keysWithDotsAction int
 }
 
-func NewYAMLFormatter(specVersion semver.Version) *YAMLFormatter {
+func NewYAMLFormatter(keysWithDotsAction int) *YAMLFormatter {
 	return &YAMLFormatter{
-		specVersion: specVersion,
+		keysWithDotsAction: keysWithDotsAction,
 	}
 }
 
@@ -33,9 +32,7 @@ func (f *YAMLFormatter) Format(content []byte) ([]byte, bool, error) {
 		return nil, false, fmt.Errorf("unmarshalling YAML file failed: %w", err)
 	}
 
-	if !f.specVersion.LessThan(semver.MustParse("3.0.0")) {
-		extendNestedObjects(&node)
-	}
+	applyActionOnKeysWithDots(&node, f.keysWithDotsAction)
 
 	var b bytes.Buffer
 	encoder := yaml.NewEncoder(&b)
@@ -55,6 +52,15 @@ func (f *YAMLFormatter) Format(content []byte) ([]byte, bool, error) {
 	return formatted, string(content) == string(formatted), nil
 }
 
+func applyActionOnKeysWithDots(node *yaml.Node, action int) {
+	switch action {
+	case KeysWithDotActionNested:
+		extendNestedObjects(node)
+	case KeysWithDotActionNone:
+		// Nothing to do.
+	}
+}
+
 func extendNestedObjects(node *yaml.Node) {
 	if node.Kind == yaml.MappingNode {
 		extendMapNode(node)
diff --git a/internal/formatter/yaml_formatter_test.go b/internal/formatter/yaml_formatter_test.go
index d714e2c92..c75f357e5 100644
--- a/internal/formatter/yaml_formatter_test.go
+++ b/internal/formatter/yaml_formatter_test.go
@@ -7,7 +7,6 @@ package formatter
 import (
 	"testing"
 
-	"github.com/Masterminds/semver/v3"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -104,9 +103,7 @@ es.other.level: 13`,
 		},
 	}
 
-	sv := semver.MustParse("3.0.0")
-	formatter := NewYAMLFormatter(*sv).Format
-
+	formatter := NewYAMLFormatter(KeysWithDotActionNested).Format
 	for _, c := range cases {
 		t.Run(c.title, func(t *testing.T) {
 			result, _, err := formatter([]byte(c.doc))
diff --git a/internal/packages/changelog/yaml.go b/internal/packages/changelog/yaml.go
index 53a8eb36b..c5579c990 100644
--- a/internal/packages/changelog/yaml.go
+++ b/internal/packages/changelog/yaml.go
@@ -125,7 +125,7 @@ func formatResult(result interface{}) ([]byte, error) {
 	if err != nil {
 		return nil, errors.New("failed to encode")
 	}
-	yamlFormatter := &formatter.YAMLFormatter{}
+	yamlFormatter := formatter.NewYAMLFormatter(formatter.KeysWithDotActionNone)
 	d, _, err = yamlFormatter.Format(d)
 	if err != nil {
 		return nil, errors.New("failed to format")