diff --git a/tests/e2e/v2store_deprecation_test.go b/tests/e2e/v2store_deprecation_test.go
index 99628cd54e3..3654b7442ac 100644
--- a/tests/e2e/v2store_deprecation_test.go
+++ b/tests/e2e/v2store_deprecation_test.go
@@ -28,6 +28,7 @@ import (
 	"go.uber.org/zap"
 	"go.uber.org/zap/zaptest"
 
+	"go.etcd.io/etcd/api/v3/version"
 	"go.etcd.io/etcd/client/pkg/v3/fileutil"
 	"go.etcd.io/etcd/pkg/v3/expect"
 	"go.etcd.io/etcd/server/v3/etcdserver"
@@ -237,27 +238,40 @@ func filterSnapshotFiles(path string) bool {
 	return strings.HasSuffix(path, ".snap")
 }
 
-func assertSnapshotsMatch(t testing.TB, firstDataDir, secondDataDir string, patch func([]byte) []byte) {
+func assertSnapshotsMatch(t testing.TB, oldMemberDataDir, newMemberDataDir string, patch func([]byte) []byte) {
 	lg := zaptest.NewLogger(t)
-	firstFiles, err := fileutil.ListFiles(firstDataDir, filterSnapshotFiles)
+	oldMemberSnapshots, err := fileutil.ListFiles(oldMemberDataDir, filterSnapshotFiles)
 	if err != nil {
 		t.Fatal(err)
 	}
-	secondFiles, err := fileutil.ListFiles(secondDataDir, filterSnapshotFiles)
+	newMemberSnapshots, err := fileutil.ListFiles(newMemberDataDir, filterSnapshotFiles)
 	if err != nil {
 		t.Fatal(err)
 	}
-	assert.NotEmpty(t, firstFiles)
-	assert.NotEmpty(t, secondFiles)
-	assert.Equal(t, len(firstFiles), len(secondFiles))
-	sort.Strings(firstFiles)
-	sort.Strings(secondFiles)
-	for i := 0; i < len(firstFiles); i++ {
-		firstSnapshot, err := snap.Read(lg, firstFiles[i])
+	assert.NotEmpty(t, oldMemberSnapshots)
+	assert.NotEmpty(t, newMemberSnapshots)
+	sort.Strings(oldMemberSnapshots)
+	sort.Strings(newMemberSnapshots)
+
+	currVer, err := e2e.GetVersionFromBinary(e2e.BinPath.Etcd)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	// Starting from v3.6, etcd might create an extra snapshot file (appliedIndex == 1) on server startup.
+	// Except for this, other snapshot files should be the same as in old versions.
+	if (version.V3_6.Equal(*currVer) || version.V3_6.LessThan(*currVer)) && len(oldMemberSnapshots) < len(newMemberSnapshots) {
+		// Remove the extra snapshot file
+		newMemberSnapshots = newMemberSnapshots[1:]
+	}
+
+	assert.Equal(t, len(oldMemberSnapshots), len(newMemberSnapshots))
+	for i := 0; i < len(oldMemberSnapshots); i++ {
+		firstSnapshot, err := snap.Read(lg, oldMemberSnapshots[i])
 		if err != nil {
 			t.Fatal(err)
 		}
-		secondSnapshot, err := snap.Read(lg, secondFiles[i])
+		secondSnapshot, err := snap.Read(lg, newMemberSnapshots[i])
 		if err != nil {
 			t.Fatal(err)
 		}