diff --git a/cmd/integration/commands/idx_verify.go b/cmd/integration/commands/idx_verify.go
new file mode 100644
index 00000000000..4dc573aa6a6
--- /dev/null
+++ b/cmd/integration/commands/idx_verify.go
@@ -0,0 +1,176 @@
+package commands
+
+import (
+	"bytes"
+	"io/fs"
+	"log"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"github.com/erigontech/erigon-lib/common"
+	"github.com/erigontech/erigon-lib/common/hexutility"
+	"github.com/erigontech/erigon-lib/config3"
+	"github.com/erigontech/erigon-lib/recsplit"
+	"github.com/erigontech/erigon-lib/recsplit/eliasfano32"
+	"github.com/erigontech/erigon-lib/recsplit/multiencseq"
+	"github.com/erigontech/erigon-lib/seg"
+	"github.com/spf13/cobra"
+)
+
+var idxVerify = &cobra.Command{
+	Use:   "idx_verify",
+	Short: "After a genesis sync + snapshot regen, deep compare original and optimized .ef files of 2 E3 instances",
+	Run: func(cmd *cobra.Command, args []string) {
+		ctx, _ := common.RootContext()
+
+		sourceIdxPath := filepath.Join(sourceDirCli, "snapshots", "idx")
+		sourceIdxDir := os.DirFS(sourceIdxPath)
+
+		files, err := fs.ReadDir(sourceIdxDir, ".")
+		if err != nil {
+			log.Fatalf("Failed to read directory contents: %v", err)
+		}
+
+		log.Println("Comparing idx files:")
+		for _, file := range files {
+			if file.IsDir() || !strings.HasSuffix(file.Name(), ".ef") {
+				continue
+			}
+
+			log.Printf("Deep checking file %s...", file.Name())
+
+			efInfo, err := parseEFFilename(file.Name())
+			if err != nil {
+				log.Fatalf("Failed to parse file info: %v", err)
+			}
+			baseTxNum := efInfo.startStep * config3.DefaultStepSize
+
+			targetEfi, err := recsplit.OpenIndex(targetDirCli + "/snapshots/accessor/" + file.Name() + "i")
+			if err != nil {
+				log.Fatalf("Failed to open index: %v", err)
+			}
+			defer targetEfi.Close()
+
+			targetEfiReader := targetEfi.GetReaderFromPool()
+			defer targetEfiReader.Close()
+
+			// original .ef file
+			sourceIdx, err := seg.NewDecompressor(sourceDirCli + "/snapshots/idx/" + file.Name())
+			if err != nil {
+				log.Fatalf("Failed to open decompressor: %v", err)
+			}
+			defer sourceIdx.Close()
+
+			// reencoded optimized .ef file
+			targetIdx, err := seg.NewDecompressor(targetDirCli + "/snapshots/idx/" + file.Name())
+			if err != nil {
+				log.Fatalf("Failed to open decompressor: %v", err)
+			}
+			defer targetIdx.Close()
+
+			g := sourceIdx.MakeGetter()
+			sourceReader := seg.NewReader(g, seg.CompressNone)
+			sourceReader.Reset(0)
+
+			g = targetIdx.MakeGetter()
+			targetReader := seg.NewReader(g, seg.CompressNone)
+			targetReader.Reset(0)
+
+			prevKeyOffset := uint64(0)
+			for sourceReader.HasNext() {
+				if !targetReader.HasNext() {
+					log.Fatal("target reader doesn't have next!")
+				}
+
+				sourceK, _ := sourceReader.Next(nil)
+				targetK, _ := targetReader.Next(nil)
+				if !bytes.Equal(sourceK, targetK) {
+					log.Fatalf("key mismatch!")
+				}
+
+				if !sourceReader.HasNext() {
+					log.Fatal("source reader doesn't have next!")
+				}
+				if !targetReader.HasNext() {
+					log.Fatal("target reader doesn't have next!")
+				}
+
+				// source/target semantic value comparison
+				sourceV, _ := sourceReader.Next(nil)
+				targetV, nextKeyOffset := targetReader.Next(nil)
+				if !compareSequences(sourceV, targetV, baseTxNum) {
+					log.Fatalf("value mismatch!")
+				}
+
+				// checks new efi lookup points to the same value
+				offset, found := targetEfiReader.TwoLayerLookup(targetK)
+				if !found {
+					log.Fatalf("key %v not found in efi", hexutility.Encode(targetK))
+				}
+				if offset != prevKeyOffset {
+					log.Fatalf("offset mismatch: %d != %d", offset, prevKeyOffset)
+				}
+				prevKeyOffset = nextKeyOffset
+
+				select {
+				case <-ctx.Done():
+					return
+				default:
+				}
+			}
+			sourceIdx.Close()
+			targetIdx.Close()
+			targetEfiReader.Close()
+			targetEfi.Close()
+		}
+	},
+}
+
+func compareSequences(sourceV, targetV []byte, baseTxNum uint64) bool {
+	sourceEf, _ := eliasfano32.ReadEliasFano(sourceV)
+	targetSeq := multiencseq.ReadMultiEncSeq(baseTxNum, targetV)
+
+	if targetSeq.Count() > sourceEf.Count() {
+		log.Print("Optimized eliasfano is longer")
+		return false
+	}
+	if sourceEf.Count() > targetSeq.Count() {
+		log.Print("Optimized eliasfano is shorter")
+		return false
+	}
+
+	sourceIt := sourceEf.Iterator()
+	targetIt := targetSeq.Iterator(0)
+	for sourceIt.HasNext() {
+		sourceN, err := sourceIt.Next()
+		if err != nil {
+			log.Fatalf("Failed to read next: %v", err)
+		}
+		targetN, err := targetIt.Next()
+		if err != nil {
+			log.Fatalf("Failed to read next: %v", err)
+		}
+		if sourceN != targetN {
+			log.Printf("values mismatch: source=%d target=%d", sourceN, targetN)
+			log.Printf("source=%v target=%v", hexutility.Encode(sourceV), hexutility.Encode(targetV))
+			return false
+		}
+	}
+
+	return true
+}
+
+func init() {
+	idxVerify.Flags().StringVar(&sourceDirCli, "sourcedir", "", "data directory of original E3 instance")
+	must(idxVerify.MarkFlagRequired("sourcedir"))
+	must(idxVerify.MarkFlagDirname("sourcedir"))
+
+	idxVerify.Flags().StringVar(&targetDirCli, "targetdir", "", "data directory of optimized E3 instance")
+	must(idxVerify.MarkFlagRequired("targetdir"))
+	must(idxVerify.MarkFlagDirname("targetdir"))
+
+	rootCmd.AddCommand(idxVerify)
+}
+
+var sourceDirCli, targetDirCli string