diff -u b/core/modules/migrate/src/Plugin/migrate/id_map/Sql.php b/core/modules/migrate/src/Plugin/migrate/id_map/Sql.php
--- b/core/modules/migrate/src/Plugin/migrate/id_map/Sql.php
+++ b/core/modules/migrate/src/Plugin/migrate/id_map/Sql.php
@@ -562,9 +562,11 @@
     $conditions = [];
     foreach ($this->sourceIdFields() as $field_name => $db_field) {
       if ($is_associative) {
-        // Associative $source_id_values can have fields out of order.
-        if (isset($source_id_values[$field_name])) {
-          $conditions[$db_field] = $source_id_values[$field_name];
+        if (array_key_exists($field_name, $source_id_values)) {
+          // Associative $source_id_values can have fields out of order.
+          if (isset($source_id_values[$field_name])) {
+            $conditions[$db_field] = $source_id_values[$field_name];
+          }
           unset($source_id_values[$field_name]);
         }
       }