diff --git a/pkg/core/blockchain.go b/pkg/core/blockchain.go
index 1b3a99370..3aa37943d 100644
--- a/pkg/core/blockchain.go
+++ b/pkg/core/blockchain.go
@@ -431,7 +431,8 @@ func (bc *Blockchain) JumpToState(module blockchainer.StateSync) error {
 	if err != nil {
 		return fmt.Errorf("failed to get current block: %w", err)
 	}
-	err = bc.dao.StoreAsCurrentBlock(block, nil)
+	writeBuf := io.NewBufBinWriter()
+	err = bc.dao.StoreAsCurrentBlock(block, writeBuf)
 	if err != nil {
 		return fmt.Errorf("failed to store current block: %w", err)
 	}
@@ -464,6 +465,18 @@ func (bc *Blockchain) JumpToState(module blockchainer.StateSync) error {
 		return fmt.Errorf("failed to update extensible whitelist: %w", err)
 	}
 
+	// After current state is updated, we need to remove outdated state-related data if so.
+	// The only outdated data we might have is genesis-related data, so check it.
+	if p-bc.config.MaxTraceableBlocks > 0 {
+		cache := bc.dao.GetWrapped()
+		writeBuf.Reset()
+		err = cache.DeleteBlock(bc.headerHashes[0], writeBuf)
+		if err != nil {
+			return fmt.Errorf("failed to remove outdated state data for the genesis block: %w", err)
+		}
+		// TODO: remove NEP17 transfers and NEP17 transfer info for genesis block, #2096 related.
+	}
+
 	updateBlockHeightMetric(p)
 	return nil
 }
diff --git a/pkg/core/blockchainer/state_root.go b/pkg/core/blockchainer/state_root.go
index 64f7d8b7c..9a540bda8 100644
--- a/pkg/core/blockchainer/state_root.go
+++ b/pkg/core/blockchainer/state_root.go
@@ -9,6 +9,7 @@ import (
 // StateRoot represents local state root module.
 type StateRoot interface {
 	AddStateRoot(root *state.MPTRoot) error
+	CleanStorage() error
 	CurrentLocalHeight() uint32
 	CurrentLocalStateRoot() util.Uint256
 	CurrentValidatedHeight() uint32
diff --git a/pkg/core/stateroot/module.go b/pkg/core/stateroot/module.go
index 20a3396e9..838e4717a 100644
--- a/pkg/core/stateroot/module.go
+++ b/pkg/core/stateroot/module.go
@@ -13,6 +13,7 @@ import (
 	"github.com/nspcc-dev/neo-go/pkg/core/storage"
 	"github.com/nspcc-dev/neo-go/pkg/crypto/keys"
 	"github.com/nspcc-dev/neo-go/pkg/util"
+	"github.com/nspcc-dev/neo-go/pkg/util/slice"
 	"go.uber.org/atomic"
 	"go.uber.org/zap"
 )
@@ -114,6 +115,47 @@ func (s *Module) Init(height uint32, enableRefCount bool) error {
 	return nil
 }
 
+// CleanStorage removes all MPT-related data from the storage (MPT nodes, validated stateroots)
+// except local stateroot for the current height and GC flag. This method is aimed to clean
+// outdated MPT data before state sync process can be started.
+// Note: this method is aimed to be called for genesis block only, an error is returned otherwice.
+func (s *Module) CleanStorage() error {
+	if s.localHeight.Load() != 0 {
+		return fmt.Errorf("can't clean MPT data for non-genesis block: expected local stateroot height 0, got %d", s.localHeight.Load())
+	}
+	gcKey := []byte{byte(storage.DataMPT), prefixGC}
+	gcVal, err := s.Store.Get(gcKey)
+	if err != nil {
+		return fmt.Errorf("failed to get GC flag: %w", err)
+	}
+	//
+	b := s.Store.Batch()
+	s.Store.Seek([]byte{byte(storage.DataMPT)}, func(k, _ []byte) {
+		// Must copy here, #1468.
+		key := slice.Copy(k)
+		b.Delete(key)
+	})
+	err = s.Store.PutBatch(b)
+	if err != nil {
+		return fmt.Errorf("failed to remove outdated MPT-reated items: %w", err)
+	}
+	err = s.Store.Put(gcKey, gcVal)
+	if err != nil {
+		return fmt.Errorf("failed to store GC flag: %w", err)
+	}
+	currentLocal := s.currentLocal.Load().(util.Uint256)
+	if !currentLocal.Equals(util.Uint256{}) {
+		err := s.addLocalStateRoot(s.Store, &state.MPTRoot{
+			Index: s.localHeight.Load(),
+			Root:  currentLocal,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to store current local stateroot: %w", err)
+		}
+	}
+	return nil
+}
+
 // JumpToState performs jump to the state specified by given stateroot index.
 func (s *Module) JumpToState(sr *state.MPTRoot, enableRefCount bool) error {
 	if err := s.addLocalStateRoot(s.Store, sr); err != nil {
diff --git a/pkg/core/statesync/module.go b/pkg/core/statesync/module.go
index 507fbc373..80939de1c 100644
--- a/pkg/core/statesync/module.go
+++ b/pkg/core/statesync/module.go
@@ -120,10 +120,33 @@ func (s *Module) Init(currChainHeight uint32) error {
 	if err == nil && pOld >= p-s.syncInterval {
 		// old point is still valid, so try to resync states for this point.
 		p = pOld
-	} else if s.bc.BlockHeight() > p-2*s.syncInterval {
-		// chain has already been synchronised up to old state sync point and regular blocks processing was started
-		s.syncStage = inactive
-		return nil
+	} else {
+		if s.bc.BlockHeight() > p-2*s.syncInterval {
+			// chain has already been synchronised up to old state sync point and regular blocks processing was started.
+			// Current block height is enough to start regular blocks processing.
+			s.syncStage = inactive
+			return nil
+		}
+		if err == nil {
+			// pOld was found, it is outdated, and chain wasn't completely synchronised for pOld. Need to drop the db.
+			return fmt.Errorf("state sync point %d is found in the storage, "+
+				"but sync process wasn't completed and point is outdated. Please, drop the database manually and restart the node to run state sync process", pOld)
+		}
+		if s.bc.BlockHeight() != 0 {
+			// pOld wasn't found, but blocks processing was started in a regular manner and latest stored block is too outdated
+			// to start regular blocks processing again. Need to drop the db.
+			return fmt.Errorf("current chain's height is too low to start regular blocks processing from the oldest sync point %d. "+
+				"Please, drop the database manually and restart the node to run state sync process", p-s.syncInterval)
+		}
+
+		// We've reached this point, so chain has genesis block only. As far as we can't ruin
+		// current chain's state until new state is completely fetched, outdated state-related data
+		// will be removed from storage during (*Blockchain).JumpToState(...) execution.
+		// All we need to do right now is to remove genesis-related MPT nodes.
+		err = s.bc.GetStateModule().CleanStorage()
+		if err != nil {
+			return fmt.Errorf("failed to remove outdated MPT data from storage: %w", err)
+		}
 	}
 
 	s.syncPoint = p