diff --git a/plumbing/format/index/encoder.go b/plumbing/format/index/encoder.go
index 00d4e7a31..2c94d93fc 100644
--- a/plumbing/format/index/encoder.go
+++ b/plumbing/format/index/encoder.go
@@ -14,7 +14,7 @@ import (
 
 var (
 	// EncodeVersionSupported is the range of supported index versions
-	EncodeVersionSupported uint32 = 2
+	EncodeVersionSupported uint32 = 3
 
 	// ErrInvalidTimestamp is returned by Encode if a Index with a Entry with
 	// negative timestamp values
@@ -36,9 +36,9 @@ func NewEncoder(w io.Writer) *Encoder {
 
 // Encode writes the Index to the stream of the encoder.
 func (e *Encoder) Encode(idx *Index) error {
-	// TODO: support versions v3 and v4
+	// TODO: support v4
 	// TODO: support extensions
-	if idx.Version != EncodeVersionSupported {
+	if idx.Version > EncodeVersionSupported {
 		return ErrUnsupportedVersion
 	}
 
@@ -68,8 +68,12 @@ func (e *Encoder) encodeEntries(idx *Index) error {
 		if err := e.encodeEntry(entry); err != nil {
 			return err
 		}
+		entryLength := entryHeaderLength
+		if entry.IntentToAdd || entry.SkipWorktree {
+			entryLength += 2
+		}
 
-		wrote := entryHeaderLength + len(entry.Name)
+		wrote := entryLength + len(entry.Name)
 		if err := e.padEntry(wrote); err != nil {
 			return err
 		}
@@ -79,10 +83,6 @@ func (e *Encoder) encodeEntries(idx *Index) error {
 }
 
 func (e *Encoder) encodeEntry(entry *Entry) error {
-	if entry.IntentToAdd || entry.SkipWorktree {
-		return ErrUnsupportedVersion
-	}
-
 	sec, nsec, err := e.timeToUint32(&entry.CreatedAt)
 	if err != nil {
 		return err
@@ -110,9 +110,25 @@ func (e *Encoder) encodeEntry(entry *Entry) error {
 		entry.GID,
 		entry.Size,
 		entry.Hash[:],
-		flags,
 	}
 
+	flagsFlow := []interface{}{flags}
+
+	if entry.IntentToAdd || entry.SkipWorktree {
+		var extendedFlags uint16
+
+		if entry.IntentToAdd {
+			extendedFlags |= intentToAddMask
+		}
+		if entry.SkipWorktree {
+			extendedFlags |= skipWorkTreeMask
+		}
+
+		flagsFlow = []interface{}{flags | entryExtended, extendedFlags}
+	}
+
+	flow = append(flow, flagsFlow...)
+
 	if err := binary.Write(e.w, flow...); err != nil {
 		return err
 	}
diff --git a/plumbing/format/index/encoder_test.go b/plumbing/format/index/encoder_test.go
index b7a73cb14..25c24f14f 100644
--- a/plumbing/format/index/encoder_test.go
+++ b/plumbing/format/index/encoder_test.go
@@ -57,7 +57,7 @@ func (s *IndexSuite) TestEncode(c *C) {
 }
 
 func (s *IndexSuite) TestEncodeUnsupportedVersion(c *C) {
-	idx := &Index{Version: 3}
+	idx := &Index{Version: 4}
 
 	buf := bytes.NewBuffer(nil)
 	e := NewEncoder(buf)
@@ -67,24 +67,40 @@ func (s *IndexSuite) TestEncodeUnsupportedVersion(c *C) {
 
 func (s *IndexSuite) TestEncodeWithIntentToAddUnsupportedVersion(c *C) {
 	idx := &Index{
-		Version: 2,
+		Version: 3,
 		Entries: []*Entry{{IntentToAdd: true}},
 	}
 
 	buf := bytes.NewBuffer(nil)
 	e := NewEncoder(buf)
 	err := e.Encode(idx)
-	c.Assert(err, Equals, ErrUnsupportedVersion)
+	c.Assert(err, IsNil)
+
+	output := &Index{}
+	d := NewDecoder(buf)
+	err = d.Decode(output)
+	c.Assert(err, IsNil)
+
+	c.Assert(cmp.Equal(idx, output), Equals, true)
+	c.Assert(output.Entries[0].IntentToAdd, Equals, true)
 }
 
 func (s *IndexSuite) TestEncodeWithSkipWorktreeUnsupportedVersion(c *C) {
 	idx := &Index{
-		Version: 2,
+		Version: 3,
 		Entries: []*Entry{{SkipWorktree: true}},
 	}
 
 	buf := bytes.NewBuffer(nil)
 	e := NewEncoder(buf)
 	err := e.Encode(idx)
-	c.Assert(err, Equals, ErrUnsupportedVersion)
+	c.Assert(err, IsNil)
+
+	output := &Index{}
+	d := NewDecoder(buf)
+	err = d.Decode(output)
+	c.Assert(err, IsNil)
+
+	c.Assert(cmp.Equal(idx, output), Equals, true)
+	c.Assert(output.Entries[0].SkipWorktree, Equals, true)
 }