diff --git a/packages/eden-watcher/src/indexer.ts b/packages/eden-watcher/src/indexer.ts
index 5a34bc11..c8ea1cc0 100644
--- a/packages/eden-watcher/src/indexer.ts
+++ b/packages/eden-watcher/src/indexer.ts
@@ -482,7 +482,7 @@ export class Indexer implements IndexerInterface {
   async markBlocksAsPruned (blocks: BlockProgress[]): Promise<void> {
     await this._baseIndexer.markBlocksAsPruned(blocks);
 
-    await this._graphWatcher.pruneEntities(blocks, ENTITIES);
+    await this._graphWatcher.pruneEntities(FrothyEntity, blocks, ENTITIES);
   }
 
   async pruneFrothyEntities (blockNumber: number): Promise<void> {
diff --git a/packages/graph-node/src/database.ts b/packages/graph-node/src/database.ts
index 82f8c55d..47d17bc5 100644
--- a/packages/graph-node/src/database.ts
+++ b/packages/graph-node/src/database.ts
@@ -1368,42 +1368,73 @@ export class Database {
       .execute();
   }
 
-  async pruneEntities (queryRunner: QueryRunner, blocks: BlockProgressInterface[], entityTypes: Set<new () => any>) {
+  async pruneEntities (frothyEntityType: new () => any, queryRunner: QueryRunner, blocks: BlockProgressInterface[], entityTypes: Set<new () => any>) {
     // Assumption: all blocks are at same height
     assert(blocks.length);
     const blockNumber = blocks[0].blockNumber;
     const blockHashes = blocks.map(block => block.blockHash);
 
     // Get all entities at the block height
-    const entitiesAtBlock = await Promise.all(
-      [...entityTypes].map(entityType => {
-        return this._baseDatabase.getEntities(
-          queryRunner,
-          entityType as any,
-          {
-            select: ['id'] as any,
-            where: { blockNumber }
-          }
-        );
-      })
-    );
+    const entitiesAtHeight = await this._baseDatabase.getEntities(queryRunner, frothyEntityType, { where: { blockNumber } });
 
     // Extract entity ids from result
-    const entityIds = entitiesAtBlock.map(entities => {
-      return entities.map((entity: any) => entity.id);
-    });
+    const entityIdsMap: Map<string, string[]> = new Map();
+
+    entitiesAtHeight.forEach(entity =>
+      entityIdsMap.set(
+        entity.name,
+        [...entityIdsMap.get(entity.name) || [], entity.id]
+      )
+    );
 
     // Update isPruned flag using fetched entity ids and hashes of blocks to be pruned
-    const updatePromises = [...entityTypes].map((entity, index: number) => {
+    const updatePromises = [...entityTypes].map((entity) => {
       return this.updateEntity(
         queryRunner,
         entity as any,
-        { id: In(entityIds[index]), blockHash: In(blockHashes) },
+        { id: In(entityIdsMap.get(entity.name) || []), blockHash: In(blockHashes) },
         { isPruned: true }
       );
     });
 
+    // Simultaneously update isPruned flag for all entities
     await Promise.all(updatePromises);
+
+    // Update latest entity tables with canonical entries
+    await this.updateNonCanonicalLatestEntities(queryRunner, blockNumber, blockHashes);
+  }
+
+  async updateNonCanonicalLatestEntities (queryRunner: QueryRunner, blockNumber: number, nonCanonicalBlockHashes: string[]): Promise<void> {
+    // Update latest entity tables with canonical entries
+    await Promise.all(
+      Array.from(this._entityToLatestEntityMap.entries()).map(async ([entity, latestEntity]) => {
+        // Get entries for non canonical blocks
+        const nonCanonicalLatestEntities = await this._baseDatabase.getEntities(queryRunner, latestEntity, { where: { blockHash: In(nonCanonicalBlockHashes) } });
+
+        await Promise.all(nonCanonicalLatestEntities.map(async (nonCanonicalLatestEntity: any) => {
+          // Get pruned version for the non canonical entity
+          const repo = queryRunner.manager.getRepository(entity);
+          const prunedVersion = await this._baseDatabase.getLatestPrunedEntityWithoutJoin(repo, nonCanonicalLatestEntity.id, blockNumber);
+
+          // If found, update the latestEntity entry for the id
+          // Else, delete the latestEntity entry for the id
+          if (prunedVersion) {
+            return this.updateEntity(
+              queryRunner,
+              latestEntity,
+              { id: nonCanonicalLatestEntity.id },
+              prunedVersion
+            );
+          } else {
+            return this._baseDatabase.removeEntities(
+              queryRunner,
+              latestEntity,
+              { where: { id: nonCanonicalLatestEntity.id } }
+            );
+          }
+        }));
+      })
+    );
   }
 
   async pruneFrothyEntities<Entity> (queryRunner: QueryRunner, frothyEntityType: new () => Entity, blockNumber: number): Promise<void> {
diff --git a/packages/graph-node/src/watcher.ts b/packages/graph-node/src/watcher.ts
index 206f3be6..4287569c 100644
--- a/packages/graph-node/src/watcher.ts
+++ b/packages/graph-node/src/watcher.ts
@@ -358,11 +358,11 @@ export class GraphWatcher {
     this._database.updateEntityCacheFrothyBlocks(blockProgress, this._indexer.serverConfig.clearEntitiesCacheInterval);
   }
 
-  async pruneEntities (prunedBlocks: BlockProgressInterface[], entityTypes: Set<new () => any>) {
+  async pruneEntities (frothyEntityType: new () => any, prunedBlocks: BlockProgressInterface[], entityTypes: Set<new () => any>) {
     const dbTx = await this._database.createTransactionRunner();
 
     try {
-      await this._database.pruneEntities(dbTx, prunedBlocks, entityTypes);
+      await this._database.pruneEntities(frothyEntityType, dbTx, prunedBlocks, entityTypes);
       await dbTx.commitTransaction();
     } catch (error) {
       await dbTx.rollbackTransaction();
diff --git a/packages/util/src/database.ts b/packages/util/src/database.ts
index cfce1392..417874d8 100644
--- a/packages/util/src/database.ts
+++ b/packages/util/src/database.ts
@@ -495,6 +495,20 @@ export class Database {
     return entityInPrunedRegion;
   }
 
+  async getLatestPrunedEntityWithoutJoin<Entity> (repo: Repository<Entity>, id: string, canonicalBlockNumber: number): Promise<Entity | undefined> {
+    // Filter out latest entity from pruned blocks.
+
+    const entityInPrunedRegion = await repo.createQueryBuilder('entity')
+      .where('entity.id = :id', { id })
+      .andWhere('entity.is_pruned = false')
+      .andWhere('entity.block_number <= :canonicalBlockNumber', { canonicalBlockNumber })
+      .orderBy('entity.block_number', 'DESC')
+      .limit(1)
+      .getOne();
+
+    return entityInPrunedRegion;
+  }
+
   async getFrothyRegion (queryRunner: QueryRunner, blockHash: string): Promise<{ canonicalBlockNumber: number, blockHashes: string[] }> {
     const heirerchicalQuery = `
       WITH RECURSIVE cte_query AS