diff --git a/app/code/Magento/Catalog/Model/Indexer/Product/Flat/Action/Row.php b/app/code/Magento/Catalog/Model/Indexer/Product/Flat/Action/Row.php
index 64a7c4be4e03c..5ea2b636933a3 100644
--- a/app/code/Magento/Catalog/Model/Indexer/Product/Flat/Action/Row.php
+++ b/app/code/Magento/Catalog/Model/Indexer/Product/Flat/Action/Row.php
@@ -85,10 +85,16 @@ public function execute($id = null)
         $ids = [$id];
         $linkField = $this->metadataPool->getMetadata(ProductInterface::class)->getLinkField();
 
+        $storeIds = $this->getAssignedStoreIdsOfProduct($id);
+
         $stores = $this->_storeManager->getStores();
         foreach ($stores as $store) {
             $tableExists = $this->_isFlatTableExists($store->getId());
             if ($tableExists) {
+                if (!in_array($store->getId(), $storeIds)) {
+                    $this->flatItemEraser->deleteProductsFromStore($id, $store->getId());
+                    continue;
+                }
                 $this->flatItemEraser->removeDeletedProducts($ids, $store->getId());
                 $this->flatItemEraser->removeDisabledProducts($ids, $store->getId());
             }
@@ -129,4 +135,23 @@ public function execute($id = null)
 
         return $this;
     }
+
+    /**
+     * Get list store id where the product is enable
+     *
+     * @param int $productId
+     * @return array
+     */
+    private function getAssignedStoreIdsOfProduct($productId)
+    {
+        $select = $this->_connection->select();
+        $select->from(['e' => $this->_productIndexerHelper->getTable('store')], ['e.store_id'])
+            ->where('c.product_id = ' . $productId)
+            ->joinLeft(
+                ['c' => $this->_productIndexerHelper->getTable('catalog_product_website')],
+                'e.website_id = c.website_id',
+                []
+            );
+        return $this->_connection->fetchCol($select);
+    }
 }
diff --git a/app/code/Magento/Catalog/Test/Unit/Model/Indexer/Product/Flat/Action/RowTest.php b/app/code/Magento/Catalog/Test/Unit/Model/Indexer/Product/Flat/Action/RowTest.php
index 11d07872fef91..61fad897c6418 100644
--- a/app/code/Magento/Catalog/Test/Unit/Model/Indexer/Product/Flat/Action/RowTest.php
+++ b/app/code/Magento/Catalog/Test/Unit/Model/Indexer/Product/Flat/Action/RowTest.php
@@ -160,8 +160,24 @@ public function testExecuteWithExistingFlatTablesCreatesTables()
             ->willReturn('store_flat_table');
         $this->connection->expects($this->any())->method('isTableExists')->with('store_flat_table')
             ->willReturn(true);
+        $this->connection->expects($this->any())->method('fetchCol')
+            ->willReturn(['store_id_1']);
         $this->flatItemEraser->expects($this->once())->method('removeDeletedProducts');
         $this->flatTableBuilder->expects($this->never())->method('build')->with('store_id_1', ['product_id_1']);
         $this->model->execute('product_id_1');
     }
+
+    public function testExecuteWithExistingFlatTablesRemoveProductFromStore()
+    {
+        $this->productIndexerHelper->expects($this->any())->method('getFlatTableName')
+            ->willReturn('store_flat_table');
+        $this->connection->expects($this->any())->method('isTableExists')->with('store_flat_table')
+            ->willReturn(true);
+        $this->connection->expects($this->any())->method('fetchCol')
+            ->willReturn([1]);
+        $this->flatItemEraser->expects($this->once())->method('deleteProductsFromStore');
+        $this->flatItemEraser->expects($this->never())->method('removeDeletedProducts');
+        $this->flatTableBuilder->expects($this->never())->method('build')->with('store_id_1', ['product_id_1']);
+        $this->model->execute('product_id_1');
+    }
 }