diff -u b/modules/line_item/commerce_line_item.module b/modules/line_item/commerce_line_item.module
--- b/modules/line_item/commerce_line_item.module
+++ b/modules/line_item/commerce_line_item.module
@@ -95,6 +95,27 @@
   return $hooks;
 }
 
+/**
+ * Implements hook_cron().
+ */
+function commerce_line_item_cron() {
+
+  // Cron operation to prune orphaned line items that were created
+  // but are no longer are associated with an order.
+  $query = 'SELECT line_item_id FROM {commerce_line_item} li
+    LEFT JOIN {field_data_commerce_line_items} fdcli
+    ON li.line_item_id = fdcli.commerce_line_items_line_item_id
+    WHERE fdcli.commerce_line_items_line_item_id IS NULL
+    AND li.created < :timestamp
+    ORDER BY li.order_id
+    LIMIT 100';
+
+  $line_item_ids = db_query($query, array(':timestamp' => strtotime('-1 day')))->fetchAllKeyed(0,0);
+
+  if (!empty($line_item_ids)) {
+    commerce_line_item_delete_multiple($line_item_ids);
+  }
+}
 
 /**
  * Implements hook_form_alter().
@@ -1600,20 +1621,24 @@
  */
 function commerce_line_item_commerce_order_update($order) {
   if (!empty($order->order_id)) {
-    $order_wrapper = entity_metadata_wrapper('commerce_order', $order);
+    $line_item_ids = array();
 
-    try {
+    // Load line item ids of the order to make sure they're excluded.
+    if (!empty($order->commerce_line_items)) {
+      $order_wrapper = entity_metadata_wrapper('commerce_order', $order);
       $line_item_ids = (array) $order_wrapper->commerce_line_items->raw();
-    } catch (Exception $ex) {
-      $ine_item_ids = array();
     }
+
+    // Query for line item ids that have a matching order id, but
+    // do not exist on the order.
     $orphaned_line_items = db_query('SELECT line_item_id FROM {commerce_line_item} WHERE order_id = :order_id AND line_item_id NOT IN(:line_item_ids)', array(
       ':order_id' => $order->order_id,
       ':line_item_ids' => $line_item_ids
     ))->fetchAllKeyed(0, 0);
 
-    foreach ((array) $orphaned_line_items as $orphaned_line_item) {
-      commerce_line_item_delete($orphaned_line_item);
+    // Bulk delete any line items that are orphaned.
+    if (!empty($orphaned_line_items)) {
+      commerce_line_item_delete_multiple($orphaned_line_items);
     }
   }
 }