diff --git a/beacon_node/beacon_chain/src/beacon_chain.rs b/beacon_node/beacon_chain/src/beacon_chain.rs
index bf4180547..fcd7be791 100644
--- a/beacon_node/beacon_chain/src/beacon_chain.rs
+++ b/beacon_node/beacon_chain/src/beacon_chain.rs
@@ -30,7 +30,7 @@ use crate::eth1_finalization_cache::{Eth1FinalizationCache, Eth1FinalizationData
 use crate::events::ServerSentEventHandler;
 use crate::execution_payload::{get_execution_payload, NotifyExecutionLayer, PreparePayloadHandle};
 use crate::fork_choice_signal::{ForkChoiceSignalRx, ForkChoiceSignalTx, ForkChoiceWaitResult};
-use crate::head_tracker::HeadTracker;
+use crate::head_tracker::{HeadTracker, HeadTrackerReader, SszHeadTracker};
 use crate::historical_blocks::HistoricalBlockError;
 use crate::light_client_finality_update_verification::{
     Error as LightClientFinalityUpdateError, VerifiedLightClientFinalityUpdate,
@@ -610,12 +610,19 @@ impl<T: BeaconChainTypes> BeaconChain<T> {
         let mut batch = vec![];
 
         let _head_timer = metrics::start_timer(&metrics::PERSIST_HEAD);
-        batch.push(self.persist_head_in_batch());
+
+        // Hold a lock to head_tracker until it has been persisted to disk. Otherwise there's a race
+        // condition with the pruning thread which can result in a block present in the head tracker
+        // but absent in the DB. This inconsistency halts pruning and dramastically increases disk
+        // size. Ref: https://github.com/sigp/lighthouse/issues/4773
+        let head_tracker = self.head_tracker.0.read();
+        batch.push(self.persist_head_in_batch(&head_tracker));
 
         let _fork_choice_timer = metrics::start_timer(&metrics::PERSIST_FORK_CHOICE);
         batch.push(self.persist_fork_choice_in_batch());
 
         self.store.hot_db.do_atomically(batch)?;
+        drop(head_tracker);
 
         Ok(())
     }
@@ -623,25 +630,28 @@ impl<T: BeaconChainTypes> BeaconChain<T> {
     /// Return a `PersistedBeaconChain` without reference to a `BeaconChain`.
     pub fn make_persisted_head(
         genesis_block_root: Hash256,
-        head_tracker: &HeadTracker,
+        head_tracker_reader: &HeadTrackerReader,
     ) -> PersistedBeaconChain {
         PersistedBeaconChain {
             _canonical_head_block_root: DUMMY_CANONICAL_HEAD_BLOCK_ROOT,
             genesis_block_root,
-            ssz_head_tracker: head_tracker.to_ssz_container(),
+            ssz_head_tracker: SszHeadTracker::from_map(head_tracker_reader),
         }
     }
 
     /// Return a database operation for writing the beacon chain head to disk.
-    pub fn persist_head_in_batch(&self) -> KeyValueStoreOp {
-        Self::persist_head_in_batch_standalone(self.genesis_block_root, &self.head_tracker)
+    pub fn persist_head_in_batch(
+        &self,
+        head_tracker_reader: &HeadTrackerReader,
+    ) -> KeyValueStoreOp {
+        Self::persist_head_in_batch_standalone(self.genesis_block_root, head_tracker_reader)
     }
 
     pub fn persist_head_in_batch_standalone(
         genesis_block_root: Hash256,
-        head_tracker: &HeadTracker,
+        head_tracker_reader: &HeadTrackerReader,
     ) -> KeyValueStoreOp {
-        Self::make_persisted_head(genesis_block_root, head_tracker)
+        Self::make_persisted_head(genesis_block_root, head_tracker_reader)
             .as_kv_store_op(BEACON_CHAIN_DB_KEY)
     }
 
@@ -1341,6 +1351,7 @@ impl<T: BeaconChainTypes> BeaconChain<T> {
         self.head_tracker.heads()
     }
 
+    /// Only used in tests.
     pub fn knows_head(&self, block_hash: &SignedBeaconBlockHash) -> bool {
         self.head_tracker.contains_head((*block_hash).into())
     }
diff --git a/beacon_node/beacon_chain/src/builder.rs b/beacon_node/beacon_chain/src/builder.rs
index d36d996f0..330036d43 100644
--- a/beacon_node/beacon_chain/src/builder.rs
+++ b/beacon_node/beacon_chain/src/builder.rs
@@ -805,10 +805,11 @@ where
         //
         // This *must* be stored before constructing the `BeaconChain`, so that its `Drop` instance
         // doesn't write a `PersistedBeaconChain` without the rest of the batch.
+        let head_tracker_reader = head_tracker.0.read();
         self.pending_io_batch.push(BeaconChain::<
             Witness<TSlotClock, TEth1Backend, TEthSpec, THotStore, TColdStore>,
         >::persist_head_in_batch_standalone(
-            genesis_block_root, &head_tracker
+            genesis_block_root, &head_tracker_reader
         ));
         self.pending_io_batch.push(BeaconChain::<
             Witness<TSlotClock, TEth1Backend, TEthSpec, THotStore, TColdStore>,
@@ -819,6 +820,7 @@ where
             .hot_db
             .do_atomically(self.pending_io_batch)
             .map_err(|e| format!("Error writing chain & metadata to disk: {:?}", e))?;
+        drop(head_tracker_reader);
 
         let genesis_validators_root = head_snapshot.beacon_state.genesis_validators_root();
         let genesis_time = head_snapshot.beacon_state.genesis_time();
diff --git a/beacon_node/beacon_chain/src/head_tracker.rs b/beacon_node/beacon_chain/src/head_tracker.rs
index 3fa577ff9..71e2473cd 100644
--- a/beacon_node/beacon_chain/src/head_tracker.rs
+++ b/beacon_node/beacon_chain/src/head_tracker.rs
@@ -1,4 +1,4 @@
-use parking_lot::RwLock;
+use parking_lot::{RwLock, RwLockReadGuard};
 use ssz_derive::{Decode, Encode};
 use std::collections::HashMap;
 use types::{Hash256, Slot};
@@ -16,6 +16,8 @@ pub enum Error {
 #[derive(Default, Debug)]
 pub struct HeadTracker(pub RwLock<HashMap<Hash256, Slot>>);
 
+pub type HeadTrackerReader<'a> = RwLockReadGuard<'a, HashMap<Hash256, Slot>>;
+
 impl HeadTracker {
     /// Register a block with `Self`, so it may or may not be included in a `Self::heads` call.
     ///
@@ -44,6 +46,11 @@ impl HeadTracker {
 
     /// Returns a `SszHeadTracker`, which contains all necessary information to restore the state
     /// of `Self` at some later point.
+    ///
+    /// Should ONLY be used for tests, due to the potential for database races.
+    ///
+    /// See <https://github.com/sigp/lighthouse/issues/4773>
+    #[cfg(test)]
     pub fn to_ssz_container(&self) -> SszHeadTracker {
         SszHeadTracker::from_map(&self.0.read())
     }