diff --git a/pkg/machinery/config/decoder/decoder.go b/pkg/machinery/config/decoder/decoder.go
index 0726426127..1fdca6b07a 100644
--- a/pkg/machinery/config/decoder/decoder.go
+++ b/pkg/machinery/config/decoder/decoder.go
@@ -178,7 +178,7 @@ func decode(manifest *yaml.Node) (target interface{}, err error) {
 
 //nolint:gocyclo
 func validate(target interface{}, spec *yaml.Node) error {
-	node, err := encoder.NewEncoder(target).Marshal()
+	node, err := encoder.NewEncoder(target, encoder.WithOmitEmpty(false)).Marshal()
 	if err != nil {
 		return err
 	}
diff --git a/pkg/machinery/config/decoder/decoder_test.go b/pkg/machinery/config/decoder/decoder_test.go
index 44a9919f23..6a71ceb0f0 100644
--- a/pkg/machinery/config/decoder/decoder_test.go
+++ b/pkg/machinery/config/decoder/decoder_test.go
@@ -23,10 +23,17 @@ type MockV2 struct {
 	Map   map[string]Mock `yaml:"map"`
 }
 
+type MockV3 struct {
+	Omit bool `yaml:"omit,omitempty"`
+}
+
 func init() {
 	config.Register("mock", func(version string) interface{} {
-		if version == "v1alpha2" {
+		switch version {
+		case "v1alpha2":
 			return &MockV2{}
+		case "v1alpha3":
+			return &MockV3{}
 		}
 
 		return &Mock{}
@@ -193,6 +200,22 @@ spec:
       not: working
       more: extra
       fields: here
+`),
+			},
+			want:    nil,
+			wantErr: true,
+		},
+		{
+			name: "extra zero fields in map",
+			fields: fields{
+				source: []byte(`---
+kind: mock
+version: v1alpha2
+spec:
+  map:
+    second:
+      a:
+        b: {}
 `),
 			},
 			want:    nil,
@@ -244,6 +267,17 @@ spec:
        - rshared
        - rw
      source: /var/local
+`),
+			},
+		},
+		{
+			name: "omit empty test",
+			fields: fields{
+				source: []byte(`---
+kind: mock
+version: v1alpha3
+spec:
+  omit: false
 `),
 			},
 		},
diff --git a/pkg/machinery/config/encoder/documentation.go b/pkg/machinery/config/encoder/documentation.go
index a3343ada2e..7525d1dcc9 100644
--- a/pkg/machinery/config/encoder/documentation.go
+++ b/pkg/machinery/config/encoder/documentation.go
@@ -194,7 +194,7 @@ func addComments(node *yaml.Node, doc *Doc, comments ...int) {
 }
 
 //nolint:gocyclo
-func renderExample(key string, doc *Doc, flags CommentsFlags) string {
+func renderExample(key string, doc *Doc, options *Options) string {
 	if doc == nil {
 		return ""
 	}
@@ -216,7 +216,7 @@ func renderExample(key string, doc *Doc, flags CommentsFlags) string {
 
 		e.Populate(i)
 
-		node, err := toYamlNode(defaultValue, flags)
+		node, err := toYamlNode(defaultValue, options)
 		if err != nil {
 			continue
 		}
@@ -224,13 +224,13 @@ func renderExample(key string, doc *Doc, flags CommentsFlags) string {
 		if key != "" {
 			node, err = toYamlNode(map[string]*yaml.Node{
 				key: node,
-			}, flags)
+			}, options)
 			if err != nil {
 				continue
 			}
 		}
 
-		if i == 0 && flags.enabled(CommentsDocs) {
+		if i == 0 && options.Comments.enabled(CommentsDocs) {
 			addComments(node, doc, HeadComment, LineComment)
 		}
 
diff --git a/pkg/machinery/config/encoder/encoder.go b/pkg/machinery/config/encoder/encoder.go
index 76869f51a7..4aaadc1c32 100644
--- a/pkg/machinery/config/encoder/encoder.go
+++ b/pkg/machinery/config/encoder/encoder.go
@@ -28,7 +28,7 @@ func NewEncoder(value interface{}, opts ...Option) *Encoder {
 
 // Marshal converts value to YAML-serializable value (suitable for MarshalYAML).
 func (e *Encoder) Marshal() (*yaml.Node, error) {
-	node, err := toYamlNode(e.value, e.options.Comments)
+	node, err := toYamlNode(e.value, e.options)
 	if err != nil {
 		return nil, err
 	}
@@ -108,9 +108,11 @@ func isNil(value reflect.Value) bool {
 }
 
 //nolint:gocyclo,cyclop
-func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
+func toYamlNode(in interface{}, options *Options) (*yaml.Node, error) {
 	node := &yaml.Node{}
 
+	flags := options.Comments
+
 	// do not wrap yaml.Node into yaml.Node
 	if n, ok := in.(*yaml.Node); ok {
 		return n, nil
@@ -118,7 +120,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 
 	// if input implements yaml.Marshaler we should use that marshaller instead
 	// same way as regular yaml marshal does
-	if m, ok := in.(yaml.Marshaler); ok {
+	if m, ok := in.(yaml.Marshaler); ok && !isNil(reflect.ValueOf(in)) {
 		res, err := m.MarshalYAML()
 		if err != nil {
 			return nil, err
@@ -181,7 +183,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 			)
 
 			for _, part := range parts {
-				if part == "omitempty" && empty {
+				if part == "omitempty" && empty && options.OmitEmpty {
 					skip = true
 				}
 
@@ -218,7 +220,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 			if empty && flags.enabled(CommentsExamples) && fieldDoc != nil {
 				if skip {
 					// render example to be appended to the end of the rendered struct
-					example := renderExample(fieldName, fieldDoc, flags)
+					example := renderExample(fieldName, fieldDoc, options)
 
 					if example != "" {
 						examples = append(examples, example)
@@ -228,7 +230,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 					fieldDocCopy := *fieldDoc
 					fieldDocCopy.Comments = [3]string{}
 
-					inlineExample = renderExample("", &fieldDocCopy, flags)
+					inlineExample = renderExample("", &fieldDocCopy, options)
 				}
 			}
 
@@ -242,7 +244,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 			}
 
 			if inline {
-				child, err := toYamlNode(value, flags)
+				child, err := toYamlNode(value, options)
 				if err != nil {
 					return nil, err
 				}
@@ -250,7 +252,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 				if child.Kind == yaml.MappingNode || child.Kind == yaml.SequenceNode {
 					appendNodes(node, child.Content...)
 				}
-			} else if err := addToMap(node, fieldDoc, fieldName, value, style, flags); err != nil {
+			} else if err := addToMap(node, fieldDoc, fieldName, value, style, options); err != nil {
 				return nil, err
 			}
 
@@ -287,7 +289,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 			element := v.MapIndex(k)
 			value := element.Interface()
 
-			if err := addToMap(node, nil, k.Interface(), value, 0, flags); err != nil {
+			if err := addToMap(node, nil, k.Interface(), value, 0, options); err != nil {
 				return nil, err
 			}
 		}
@@ -300,7 +302,7 @@ func toYamlNode(in interface{}, flags CommentsFlags) (*yaml.Node, error) {
 
 			var err error
 
-			nodes[i], err = toYamlNode(element.Interface(), flags)
+			nodes[i], err = toYamlNode(element.Interface(), options)
 			if err != nil {
 				return nil, err
 			}
@@ -323,20 +325,20 @@ func appendNodes(dest *yaml.Node, nodes ...*yaml.Node) {
 	dest.Content = append(dest.Content, nodes...)
 }
 
-func addToMap(dest *yaml.Node, doc *Doc, fieldName, in interface{}, style yaml.Style, flags CommentsFlags) error {
-	key, err := toYamlNode(fieldName, flags)
+func addToMap(dest *yaml.Node, doc *Doc, fieldName, in interface{}, style yaml.Style, options *Options) error {
+	key, err := toYamlNode(fieldName, options)
 	if err != nil {
 		return err
 	}
 
-	value, err := toYamlNode(in, flags)
+	value, err := toYamlNode(in, options)
 	if err != nil {
 		return err
 	}
 
 	value.Style = style
 
-	if flags.enabled(CommentsDocs) {
+	if options.Comments.enabled(CommentsDocs) {
 		addComments(key, doc, HeadComment, FootComment)
 		addComments(value, doc, LineComment)
 	}
diff --git a/pkg/machinery/config/encoder/markdown.go b/pkg/machinery/config/encoder/markdown.go
index cd1252a68c..4b62c549d6 100644
--- a/pkg/machinery/config/encoder/markdown.go
+++ b/pkg/machinery/config/encoder/markdown.go
@@ -180,7 +180,7 @@ func encodeYaml(in interface{}, name string) string {
 		}
 	}
 
-	node, err := toYamlNode(in, CommentsAll)
+	node, err := toYamlNode(in, newOptions(WithComments(CommentsAll)))
 	if err != nil {
 		return fmt.Sprintf("yaml encoding failed %s", err)
 	}
diff --git a/pkg/machinery/config/encoder/options.go b/pkg/machinery/config/encoder/options.go
index e73b2317f1..456d84f1ae 100644
--- a/pkg/machinery/config/encoder/options.go
+++ b/pkg/machinery/config/encoder/options.go
@@ -24,12 +24,14 @@ const (
 
 // Options defines encoder config.
 type Options struct {
-	Comments CommentsFlags
+	Comments  CommentsFlags
+	OmitEmpty bool
 }
 
 func newOptions(opts ...Option) *Options {
 	res := &Options{
-		Comments: CommentsAll,
+		Comments:  CommentsAll,
+		OmitEmpty: true,
 	}
 
 	for _, o := range opts {
@@ -48,3 +50,10 @@ func WithComments(flags CommentsFlags) Option {
 		o.Comments = flags
 	}
 }
+
+// WithOmitEmpty toggles omitempty handling.
+func WithOmitEmpty(value bool) Option {
+	return func(o *Options) {
+		o.OmitEmpty = value
+	}
+}