diff --git a/Network/Haskoin/Node/BlockChain.hs b/Network/Haskoin/Node/BlockChain.hs
--- a/Network/Haskoin/Node/BlockChain.hs
+++ b/Network/Haskoin/Node/BlockChain.hs
@@ -128,21 +128,27 @@
 -- rescans.
 merkleDownload
     :: (MonadLoggerIO m, MonadBaseControl IO m)
-    => NodeBlock
+    => BlockHash
     -> Word32
     -> NodeT m
        (BlockChainAction, Source (NodeT m) (Either (MerkleBlock, MerkleTxs) Tx))
-merkleDownload bh batchSize = do
+merkleDownload walletHash batchSize = do
     -- Store the best block received from the wallet for information only.
     -- This will be displayed in `hw status`
-    atomicallyNodeT $ writeTVarS sharedBestBlock bh
-    merkleCheckSync
+    merkleSyncedActions walletHash
+    walletBlockM <- runSqlNodeT $ getBlockByHash walletHash
+    walletBlock <- case walletBlockM of
+        Just walletBlock -> do
+            atomicallyNodeT $ writeTVarS sharedBestBlock walletBlock
+            return walletBlock
+        Nothing ->
+            error "Could not find wallet best block in headers"
     rescanTMVar <- asks sharedRescan
     -- Wait either for a new block to arrive or a rescan to be triggered
     $(logDebug) "Waiting for a new block or a rescan..."
     resE <- atomicallyNodeT $ orElseNodeT
         (fmap Left $ lift $ takeTMVar rescanTMVar)
-        (const (Right ()) <$> waitNewBlock (nodeHash bh))
+        (const (Right ()) <$> waitNewBlock walletHash)
     resM <- case resE of
         -- A rescan was triggered
         Left valE -> do
@@ -154,16 +160,16 @@
                 [ "Rescan condition reached:", show newValE ]
             case newValE of
                 Left ts -> tryMerkleDwnTimestamp ts batchSize
-                Right _ -> tryMerkleDwnHeight bh batchSize
+                Right _ -> tryMerkleDwnHeight walletBlock batchSize
         -- Continue download from a hash
-        Right _ -> tryMerkleDwnBlock bh batchSize
+        Right _ -> tryMerkleDwnBlock walletBlock batchSize
     case resM of
         Just res -> return res
         _ -> do
             $(logWarn) "Invalid merkleDownload result. Retrying ..."
             -- Sleep 10 seconds and retry
             liftIO $ threadDelay $ 10*1000000
-            merkleDownload bh batchSize
+            merkleDownload walletHash batchSize
   where
     waitRescan rescanTMVar valE = do
         resE <- atomicallyNodeT $ orElseNodeT
@@ -176,21 +182,30 @@
         Left ts -> waitFastCatchup ts
         Right h -> waitHeight h
 
-merkleCheckSync :: (MonadLoggerIO m, MonadBaseControl IO m)
-                => NodeT m ()
-merkleCheckSync = do
+-- | Perform some actions only when headers have been synced.
+merkleSyncedActions
+    :: (MonadLoggerIO m, MonadBaseControl IO m)
+    => BlockHash -- ^ Wallet best block
+    -> NodeT m ()
+merkleSyncedActions walletHash =
+    asks sharedSyncLock >>= \lock -> liftBaseOp_ (Lock.with lock) $ do
     -- Check if we are synced
-    (synced, mempool, ourHeight) <- atomicallyNodeT $ do
-        synced <- areBlocksSynced
-        when synced $ writeTVarS sharedMerklePeer Nothing
-        ourHeight <- nodeBlockHeight <$> readTVarS sharedBestHeader
+    (synced, mempool, header) <- atomicallyNodeT $ do
+        header <- readTVarS sharedBestHeader
+        synced <- areBlocksSynced walletHash
         mempool <- readTVarS sharedMempool
-        return (synced, mempool, ourHeight)
+        return (synced, mempool, header)
     when synced $ do
         $(logInfo) $ pack $ unwords
             [ "Merkle blocks are in sync with the"
-            , "network at height", show ourHeight
+            , "network at height", show walletHash
             ]
+        -- Prune side chains
+        bestBlock <- runSqlNodeT $ pruneChain header
+        atomicallyNodeT $ do
+            -- Update shared best header after pruning
+            writeTVarS sharedBestHeader bestBlock
+            writeTVarS sharedMerklePeer Nothing
         -- Do a mempool sync on the first merkle sync
         unless mempool $ do
             atomicallyNodeT $ do
@@ -469,8 +484,6 @@
         (synced, ourHeight) <- syncedHeight
         if synced
             then do
-                -- Check if merkles are synced
-                merkleCheckSync
                 $(logInfo) $ formatPid pid peerSessionHost $ unwords
                     [ "Block headers are in sync with the"
                     , "network at height", show ourHeight
@@ -516,12 +529,11 @@
                 , "network at height", show ourHeight
                 ]
 
-areBlocksSynced :: NodeT STM Bool
-areBlocksSynced = do
+areBlocksSynced :: BlockHash -> NodeT STM Bool
+areBlocksSynced walletHash = do
     headersSynced <- areHeadersSynced
-    bestBlock     <- readTVarS sharedBestBlock
     bestHeader    <- readTVarS sharedBestHeader
-    return $ headersSynced && nodeHash bestBlock == nodeHash bestHeader
+    return $ headersSynced && walletHash == nodeHash bestHeader
 
 -- Check if the block headers are synced with the network height
 areHeadersSynced :: NodeT STM Bool
diff --git a/Network/Haskoin/Node/HeaderTree.hs b/Network/Haskoin/Node/HeaderTree.hs
--- a/Network/Haskoin/Node/HeaderTree.hs
+++ b/Network/Haskoin/Node/HeaderTree.hs
@@ -37,6 +37,7 @@
 , connectHeader
 , connectHeaders
 , blockLocator
+, pruneChain
 ) where
 
 import           Control.Monad                         (foldM, forM, unless,
@@ -616,8 +617,7 @@
 evalNewChain _ [] = error "You find yourself in the dungeon of missing blocks"
 evalNewChain best newNodes
     | buildsOnBest = do
-        pruneChain best
-        return $ BestChain $ map (\n -> n{ nodeBlockChain = 0 }) newNodes
+        return $ BestChain newNodes
     | nodeBlockWork (last newNodes) > nodeBlockWork best = do
         (split, old, new) <- splitChains (best, 0) (head newNodes, 0)
         return $ ChainReorg split old (new ++ tail newNodes)
@@ -629,16 +629,15 @@
   where
     buildsOnBest = nodePrev (head newNodes) == nodeHash best
 
+-- | Remove all other chains from database and return updated best block node.
 pruneChain :: MonadIO m
            => NodeBlock
-           -> SqlPersistT m ()
-pruneChain best = do
-    when (nodeBlockChain best /= 0) $ do
-        forks <- reverse <$> getPivots best
-        delete $ from $ \t -> do
-            where_ $ not_ (chainPathQuery t forks)
-                 &&. t ^. NodeBlockHeight <=. val (nodeBlockHeight best)
-        update $ \t -> do
-            set t [ NodeBlockChain =. val 0 ]
-            where_ $ t ^. NodeBlockHeight <=. val (nodeBlockHeight best)
-                 &&. t ^. NodeBlockChain  !=. val 0
+           -> SqlPersistT m NodeBlock
+pruneChain best = if (nodeBlockChain best == 0) then return best else do
+    forks <- reverse <$> getPivots best
+    delete $ from $ \t -> where_ $ not_ (chainPathQuery t forks)
+    update $ \t -> do
+        set t [ NodeBlockChain =. val 0 ]
+        where_ $ t ^. NodeBlockHeight <=. val (nodeBlockHeight best)
+              &&. t ^. NodeBlockChain  !=. val 0
+    return best{ nodeBlockChain = 0 }
diff --git a/haskoin-node.cabal b/haskoin-node.cabal
--- a/haskoin-node.cabal
+++ b/haskoin-node.cabal
@@ -1,5 +1,5 @@
 name:                  haskoin-node
-version:               0.3.0
+version:               0.3.1
 synopsis:
     Implementation of a Bitoin node.
 description: