diff --git a/store/v2/storage/pebbledb/batch.go b/store/v2/storage/pebbledb/batch.go
index 101986878c8..fdd58f44743 100644
--- a/store/v2/storage/pebbledb/batch.go
+++ b/store/v2/storage/pebbledb/batch.go
@@ -17,6 +17,17 @@ type Batch struct {
 	batch   *pebble.Batch
 	version uint64
 	sync    bool
+	size    int
+}
+
+const (
+	oneIf64Bit     = ^uint(0) >> 63
+	maxUint32OrInt = (1<<31)<<oneIf64Bit - 1
+	maxVarintLen32 = 5
+)
+
+func keyValueSize(key, value []byte) int {
+	return len(key) + len(value) + 1 + 2*maxVarintLen32
 }
 
 func NewBatch(storage *pebble.DB, version uint64, sync bool) (*Batch, error) {
@@ -34,6 +45,7 @@ func NewBatch(storage *pebble.DB, version uint64, sync bool) (*Batch, error) {
 		batch:   batch,
 		version: version,
 		sync:    sync,
+		size:    keyValueSize([]byte(latestVersionKey), versionBz[:]),
 	}, nil
 }
 
@@ -50,9 +62,20 @@ func (b *Batch) set(storeKey []byte, tombstone uint64, key, value []byte) error
 	prefixedKey := MVCCEncode(prependStoreKey(storeKey, key), b.version)
 	prefixedVal := MVCCEncode(value, tombstone)
 
+	size := keyValueSize(prefixedKey, prefixedVal)
+	if b.size+size > maxUint32OrInt {
+		// 4 GB is huge, probably genesis; flush and reset
+		if err := b.batch.Commit(&pebble.WriteOptions{Sync: b.sync}); err != nil {
+			return fmt.Errorf("max batch size exceed: failed to write PebbleDB batch: %w", err)
+		}
+		b.batch.Reset()
+		b.size = 0
+	}
+
 	if err := b.batch.Set(prefixedKey, prefixedVal, nil); err != nil {
 		return fmt.Errorf("failed to write PebbleDB batch: %w", err)
 	}
+	b.size += size
 
 	return nil
 }
diff --git a/store/v2/storage/pebbledb/db.go b/store/v2/storage/pebbledb/db.go
index 1547dba102d..20fc3f11c7f 100644
--- a/store/v2/storage/pebbledb/db.go
+++ b/store/v2/storage/pebbledb/db.go
@@ -238,11 +238,14 @@ func (db *Database) Prune(version uint64) (err error) {
 			return fmt.Errorf("invalid PebbleDB MVCC key: %s", prefixedKey)
 		}
 
-		keyVersion, err := decodeUint64Ascending(verBz)
-		if err != nil {
-			return fmt.Errorf("failed to decode key version: %w", err)
+		var keyVersion uint64
+		// handle version 0 (no version prefix)
+		if len(verBz) > 0 {
+			keyVersion, err = decodeUint64Ascending(verBz)
+			if err != nil {
+				return fmt.Errorf("failed to decode key version: %w", err)
+			}
 		}
-
 		// seek to next key if we are at a version which is higher than prune height
 		if keyVersion > version {
 			itr.NextPrefix()
@@ -432,9 +435,13 @@ func getMVCCSlice(db *pebble.DB, storeKey, key []byte, version uint64) ([]byte,
 		return nil, fmt.Errorf("invalid PebbleDB MVCC key: %s", itr.Key())
 	}
 
-	keyVersion, err := decodeUint64Ascending(vBz)
-	if err != nil {
-		return nil, fmt.Errorf("failed to decode key version: %w", err)
+	var keyVersion uint64
+	// handle version 0 (no version prefix)
+	if len(vBz) > 0 {
+		keyVersion, err = decodeUint64Ascending(vBz)
+		if err != nil {
+			return nil, fmt.Errorf("failed to decode key version: %w", err)
+		}
 	}
 	if keyVersion > version {
 		return nil, fmt.Errorf("key version too large: %d", keyVersion)
diff --git a/store/v2/storage/pebbledb/iterator.go b/store/v2/storage/pebbledb/iterator.go
index 6cafe196a20..2401ab4ef00 100644
--- a/store/v2/storage/pebbledb/iterator.go
+++ b/store/v2/storage/pebbledb/iterator.go
@@ -216,15 +216,20 @@ func (itr *iterator) DebugRawIterate() {
 		valid = itr.source.SeekLT(MVCCEncode(firstKey, itr.version+1))
 	}
 
+	var err error
 	for valid {
 		key, vBz, ok := SplitMVCCKey(itr.source.Key())
 		if !ok {
 			panic(fmt.Sprintf("invalid PebbleDB MVCC key: %s", itr.source.Key()))
 		}
 
-		version, err := decodeUint64Ascending(vBz)
-		if err != nil {
-			panic(fmt.Errorf("failed to decode key version: %w", err))
+		var version uint64
+		// handle version 0 (no version prefix)
+		if len(vBz) > 0 {
+			version, err = decodeUint64Ascending(vBz)
+			if err != nil {
+				panic(fmt.Errorf("failed to decode key version: %w", err))
+			}
 		}
 
 		val, tombBz, ok := SplitMVCCKey(itr.source.Value())