diff --git a/bookkeeper-server/src/main/java/org/apache/bookkeeper/bookie/storage/ldb/EntryLocationIndex.java b/bookkeeper-server/src/main/java/org/apache/bookkeeper/bookie/storage/ldb/EntryLocationIndex.java
index 53e37a263cf..21b87e2be96 100644
--- a/bookkeeper-server/src/main/java/org/apache/bookkeeper/bookie/storage/ldb/EntryLocationIndex.java
+++ b/bookkeeper-server/src/main/java/org/apache/bookkeeper/bookie/storage/ldb/EntryLocationIndex.java
@@ -27,6 +27,7 @@
 import java.nio.file.FileSystems;
 import java.util.Map.Entry;
 import java.util.Set;
+import java.util.concurrent.TimeUnit;
 
 import org.apache.bookkeeper.bookie.Bookie;
 import org.apache.bookkeeper.bookie.EntryLocation;
@@ -188,6 +189,8 @@ public void delete(long ledgerId) throws IOException {
         deletedLedgers.add(ledgerId);
     }
 
+    private static final int DELETE_ENTRIES_BATCH_SIZE = 100000;
+
     public void removeOffsetFromDeletedLedgers() throws IOException {
         LongPairWrapper firstKeyWrapper = LongPairWrapper.get(-1, -1);
         LongPairWrapper lastKeyWrapper = LongPairWrapper.get(-1, -1);
@@ -200,6 +203,10 @@ public void removeOffsetFromDeletedLedgers() throws IOException {
         }
 
         log.info("Deleting indexes for ledgers: {}", ledgersToDelete);
+        long startTime = System.nanoTime();
+        long deletedEntries = 0;
+        long deletedEntriesInBatch = 0;
+
         Batch batch = locationsDb.newBatch();
 
         try {
@@ -211,20 +218,58 @@ public void removeOffsetFromDeletedLedgers() throws IOException {
                 firstKeyWrapper.set(ledgerId, 0);
                 lastKeyWrapper.set(ledgerId, Long.MAX_VALUE);
 
-                batch.deleteRange(firstKeyWrapper.array, lastKeyWrapper.array);
-            }
+                Entry<byte[], byte[]> firstKeyRes = locationsDb.getCeil(firstKeyWrapper.array);
+                if (firstKeyRes == null || ArrayUtil.getLong(firstKeyRes.getKey(), 0) != ledgerId) {
+                    // No entries found for ledger
+                    if (log.isDebugEnabled()) {
+                        log.debug("No entries found for ledger {}", ledgerId);
+                    }
+                    continue;
+                }
 
-            batch.flush();
+                long firstEntryId = ArrayUtil.getLong(firstKeyRes.getKey(), 8);
+                long lastEntryId = getLastEntryInLedgerInternal(ledgerId);
+                if (log.isDebugEnabled()) {
+                    log.debug("Deleting index for ledger {} entries ({} -> {})",
+                            ledgerId, firstEntryId, lastEntryId);
+                }
 
-            // Removed from pending set
-            for (long ledgerId : ledgersToDelete) {
-                deletedLedgers.remove(ledgerId);
+                // Iterate over all the keys and remove each of them
+                for (long entryId = firstEntryId; entryId <= lastEntryId; entryId++) {
+                    keyToDelete.set(ledgerId, entryId);
+                    if (log.isDebugEnabled()) {
+                        log.debug("Deleting index for ({}, {})", keyToDelete.getFirst(), keyToDelete.getSecond());
+                    }
+                    batch.remove(keyToDelete.array);
+                    ++deletedEntriesInBatch;
+                    ++deletedEntries;
+                }
+
+                if (deletedEntriesInBatch > DELETE_ENTRIES_BATCH_SIZE) {
+                    batch.flush();
+                    batch.clear();
+                    deletedEntriesInBatch = 0;
+                }
             }
         } finally {
-            firstKeyWrapper.recycle();
-            lastKeyWrapper.recycle();
-            keyToDelete.recycle();
-            batch.close();
+            try {
+                batch.flush();
+                batch.clear();
+            } finally {
+
+                firstKeyWrapper.recycle();
+                lastKeyWrapper.recycle();
+                keyToDelete.recycle();
+                batch.close();
+            }
+        }
+
+        log.info("Deleted indexes for {} entries from {} ledgers in {} seconds", deletedEntries, ledgersToDelete.size(),
+                TimeUnit.NANOSECONDS.toMillis(System.nanoTime() - startTime) / 1000.0);
+
+        // Removed from pending set
+        for (long ledgerId : ledgersToDelete) {
+            deletedLedgers.remove(ledgerId);
         }
     }