diff --git a/pkg/core/blockchain.go b/pkg/core/blockchain.go
index 91ed7da26..c9fe95e5e 100644
--- a/pkg/core/blockchain.go
+++ b/pkg/core/blockchain.go
@@ -348,6 +348,43 @@ func (bc *Blockchain) init() error {
 		return fmt.Errorf("can't init cache for Management native contract: %w", err)
 	}
 
+	// Check autogenerated native contracts' manifests and NEFs against the stored ones.
+	// Need to be done after native Management cache initialisation to be able to get
+	// contract state from DAO via high-level bc API.
+	for _, c := range bc.contracts.Contracts {
+		md := c.Metadata()
+		history := md.UpdateHistory
+		if len(history) == 0 || history[0] > bHeight {
+			continue
+		}
+		storedCS := bc.GetContractState(md.Hash)
+		if storedCS == nil {
+			return fmt.Errorf("native contract %s is not stored", md.Name)
+		}
+		w := io.NewBufBinWriter()
+		storedCS.EncodeBinary(w.BinWriter)
+		if w.Err != nil {
+			return fmt.Errorf("failed to check native %s state against autogenerated one: %w", md.Name, w.Err)
+		}
+		buff := w.Bytes()
+		storedCSBytes := make([]byte, len(buff))
+		copy(storedCSBytes, buff)
+		w.Reset()
+		autogenCS := &state.Contract{
+			ContractBase:  md.ContractBase,
+			UpdateCounter: storedCS.UpdateCounter, // it can be restored only from the DB, so use the stored value.
+		}
+		autogenCS.EncodeBinary(w.BinWriter)
+		if w.Err != nil {
+			return fmt.Errorf("failed to check native %s state against autogenerated one: %w", md.Name, w.Err)
+		}
+		autogenCSBytes := w.Bytes()
+		if !bytes.Equal(storedCSBytes, autogenCSBytes) {
+			return fmt.Errorf("native %s: version mismatch (stored contract state differs from autogenerated one), "+
+				"try to resynchronize the node from the genesis", md.Name)
+		}
+	}
+
 	return bc.updateExtensibleWhitelist(bHeight)
 }