diff --git a/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
index 45246e3..1d49cd9 100644
--- a/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
+++ b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
@@ -1671,7 +1671,7 @@ public function countFieldData($storage_definition, $as_bool = FALSE) {
         ->fields('t', array('entity_id'))
         ->distinct(TRUE);
     }
-    else {
+    elseif ($table_mapping->allowsSharedTableStorage($storage_definition)) {
       $data_table = $this->dataTable ?: $this->baseTable;
       // @todo This check is here because system_system_info_alter() calls
       //   countFieldData(), even in KernelTestBase tests, where the schema
@@ -1697,12 +1697,17 @@ public function countFieldData($storage_definition, $as_bool = FALSE) {
         ->distinct(TRUE);
     }
 
-    // If we are performing the query just to check if the field has data
-    // limit the number of rows.
-    if ($as_bool) {
-      $query->range(0, 1);
+    // @todo Find a way to count field data also for fields having custom
+    //   storage. See https://www.drupal.org/node/2337753.
+    $count = 0;
+    if (isset($query)) {
+      // If we are performing the query just to check if the field has data
+      // limit the number of rows.
+      if ($as_bool) {
+        $query->range(0, 1);
+      }
+      $count = $query->countQuery()->execute()->fetchField();
     }
-    $count = $query->countQuery()->execute()->fetchField();
     return $as_bool ? (bool) $count : (int) $count;
   }
 
diff --git a/core/modules/system/system.module b/core/modules/system/system.module
index 2b5ca0e..bd8d031 100644
--- a/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -8,6 +8,7 @@
 use Drupal\Component\Plugin\Exception\PluginNotFoundException;
 use Drupal\Core\Block\BlockPluginInterface;
 use Drupal\Core\Cache\Cache;
+use Drupal\Core\Entity\FieldableEntityStorageInterface;
 use Drupal\Core\Extension\Extension;
 use Drupal\Core\Extension\ExtensionDiscovery;
 use Drupal\Core\Form\FormStateInterface;
@@ -1051,13 +1052,10 @@ function system_system_info_alter(&$info, Extension $file, $type) {
             // We skip entity-defining modules, otherwise deleting all entities
             // would be required before being able to uninstall them.
             if ($entity_type->isFieldable() && $entity_type->getProvider() != $module_name) {
-              $storage_definitions = $entity_manager->getFieldStorageDefinitions($entity_type_id);
-              // @todo Make it easier to query if there are entities:
-              //   https://www.drupal.org/node/2337753.
-              $has_data = $entity_type->hasKey('id') && $entity_manager->getStorage($entity_type_id)->countFieldData($storage_definitions[$entity_type->getKey('id')], TRUE);
-              if ($has_data) {
-                foreach ($storage_definitions as $storage_definition) {
-                  if ($storage_definition->getProvider() == $module_name) {
+              $storage = $entity_manager->getStorage($entity_type_id);
+              if ($storage instanceof FieldableEntityStorageInterface) {
+                foreach ($entity_manager->getFieldStorageDefinitions($entity_type_id) as $storage_definition) {
+                  if ($storage_definition->getProvider() == $module_name && $storage->countFieldData($storage_definition, TRUE)) {
                     $info['required'] = TRUE;
                     $info['explanation'] = t('Fields type(s) in use');
                     break;