diff --git a/crates/primitives/src/checkpoints.rs b/crates/primitives/src/checkpoints.rs
index ee9baad7c0..ba460e493a 100644
--- a/crates/primitives/src/checkpoints.rs
+++ b/crates/primitives/src/checkpoints.rs
@@ -1,6 +1,6 @@
 use crate::{
     trie::{hash_builder::HashBuilderState, StoredSubNode},
-    Address, H256,
+    Address, BlockNumber, H256,
 };
 use bytes::Buf;
 use reth_codecs::{main_codec, Compact};
@@ -8,7 +8,8 @@ use reth_codecs::{main_codec, Compact};
 /// Saves the progress of Merkle stage.
 #[derive(Default, Debug, Clone, PartialEq)]
 pub struct MerkleCheckpoint {
-    // TODO: target block?
+    /// The target block number.
+    pub target_block: BlockNumber,
     /// The last hashed account key processed.
     pub last_account_key: H256,
     /// The last walker key processed.
@@ -19,6 +20,19 @@ pub struct MerkleCheckpoint {
     pub state: HashBuilderState,
 }
 
+impl MerkleCheckpoint {
+    /// Creates a new Merkle checkpoint.
+    pub fn new(
+        target_block: BlockNumber,
+        last_account_key: H256,
+        last_walker_key: Vec<u8>,
+        walker_stack: Vec<StoredSubNode>,
+        state: HashBuilderState,
+    ) -> Self {
+        Self { target_block, last_account_key, last_walker_key, walker_stack, state }
+    }
+}
+
 impl Compact for MerkleCheckpoint {
     fn to_compact<B>(self, buf: &mut B) -> usize
     where
@@ -26,6 +40,9 @@ impl Compact for MerkleCheckpoint {
     {
         let mut len = 0;
 
+        buf.put_u64(self.target_block);
+        len += 8;
+
         buf.put_slice(self.last_account_key.as_slice());
         len += self.last_account_key.len();
 
@@ -47,6 +64,8 @@ impl Compact for MerkleCheckpoint {
     where
         Self: Sized,
     {
+        let target_block = buf.get_u64();
+
         let last_account_key = H256::from_slice(&buf[..32]);
         buf.advance(32);
 
@@ -63,7 +82,16 @@ impl Compact for MerkleCheckpoint {
         }
 
         let (state, buf) = HashBuilderState::from_compact(buf, 0);
-        (MerkleCheckpoint { last_account_key, last_walker_key, walker_stack, state }, buf)
+        (
+            MerkleCheckpoint {
+                target_block,
+                last_account_key,
+                last_walker_key,
+                walker_stack,
+                state,
+            },
+            buf,
+        )
     }
 }
 
@@ -92,3 +120,30 @@ pub struct StorageHashingCheckpoint {
     /// Last transition id
     pub to: u64,
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rand::Rng;
+
+    #[test]
+    fn merkle_checkpoint_roundtrip() {
+        let mut rng = rand::thread_rng();
+        let checkpoint = MerkleCheckpoint {
+            target_block: rng.gen(),
+            last_account_key: H256::from_low_u64_be(rng.gen()),
+            last_walker_key: H256::from_low_u64_be(rng.gen()).to_vec(),
+            walker_stack: Vec::from([StoredSubNode {
+                key: H256::from_low_u64_be(rng.gen()).to_vec(),
+                nibble: Some(rng.gen()),
+                node: None,
+            }]),
+            state: HashBuilderState::default(),
+        };
+
+        let mut buf = Vec::new();
+        let encoded = checkpoint.clone().to_compact(&mut buf);
+        let (decoded, _) = MerkleCheckpoint::from_compact(&buf, encoded);
+        assert_eq!(decoded, checkpoint);
+    }
+}
diff --git a/crates/stages/src/stages/merkle.rs b/crates/stages/src/stages/merkle.rs
index ece8da5e9b..d050c48e1a 100644
--- a/crates/stages/src/stages/merkle.rs
+++ b/crates/stages/src/stages/merkle.rs
@@ -6,7 +6,7 @@ use reth_db::{
     transaction::{DbTx, DbTxMut},
 };
 use reth_interfaces::consensus;
-use reth_primitives::{hex, BlockNumber, MerkleCheckpoint, H256};
+use reth_primitives::{hex, trie::StoredSubNode, BlockNumber, MerkleCheckpoint, H256};
 use reth_provider::Transaction;
 use reth_trie::{IntermediateStateRootState, StateRoot, StateRootProgress};
 use std::{fmt::Debug, ops::DerefMut};
@@ -168,7 +168,7 @@ impl<DB: Database> Stage<DB> for MerkleStage {
             block_root
         } else if to_block - from_block > threshold || from_block == 1 {
             // if there are more blocks than threshold it is faster to rebuild the trie
-            if let Some(checkpoint) = &checkpoint {
+            if let Some(checkpoint) = checkpoint.as_ref().filter(|c| c.target_block == to_block) {
                 debug!(
                     target: "sync::stages::merkle::exec",
                     current = ?current_block,
@@ -182,8 +182,11 @@ impl<DB: Database> Stage<DB> for MerkleStage {
                     target: "sync::stages::merkle::exec",
                     current = ?current_block,
                     target = ?to_block,
+                    previous_checkpoint = ?checkpoint,
                     "Rebuilding trie"
                 );
+                // Reset the checkpoint and clear trie tables
+                self.save_execution_checkpoint(tx, None)?;
                 tx.clear::<tables::AccountsTrie>()?;
                 tx.clear::<tables::StoragesTrie>()?;
             }
@@ -195,7 +198,14 @@ impl<DB: Database> Stage<DB> for MerkleStage {
             match progress {
                 StateRootProgress::Progress(state, updates) => {
                     updates.flush(tx.deref_mut())?;
-                    self.save_execution_checkpoint(tx, Some((*state).into()))?;
+                    let checkpoint = MerkleCheckpoint::new(
+                        to_block,
+                        state.last_account_key,
+                        state.last_walker_key.hex_data,
+                        state.walker_stack.into_iter().map(StoredSubNode::from).collect(),
+                        state.hash_builder.into(),
+                    );
+                    self.save_execution_checkpoint(tx, Some(checkpoint))?;
                     return Ok(ExecOutput { stage_progress: input.stage_progress(), done: false })
                 }
                 StateRootProgress::Complete(root, updates) => {
diff --git a/crates/trie/src/progress.rs b/crates/trie/src/progress.rs
index 0164d60178..3ef851e546 100644
--- a/crates/trie/src/progress.rs
+++ b/crates/trie/src/progress.rs
@@ -1,6 +1,6 @@
 use crate::{trie_cursor::CursorSubNode, updates::TrieUpdates};
 use reth_primitives::{
-    trie::{hash_builder::HashBuilder, Nibbles, StoredSubNode},
+    trie::{hash_builder::HashBuilder, Nibbles},
     MerkleCheckpoint, H256,
 };
 
@@ -27,17 +27,6 @@ pub struct IntermediateStateRootState {
     pub last_walker_key: Nibbles,
 }
 
-impl From<IntermediateStateRootState> for MerkleCheckpoint {
-    fn from(value: IntermediateStateRootState) -> Self {
-        Self {
-            last_account_key: value.last_account_key,
-            last_walker_key: value.last_walker_key.hex_data,
-            walker_stack: value.walker_stack.into_iter().map(StoredSubNode::from).collect(),
-            state: value.hash_builder.into(),
-        }
-    }
-}
-
 impl From<MerkleCheckpoint> for IntermediateStateRootState {
     fn from(value: MerkleCheckpoint) -> Self {
         Self {