diff -u b/core/lib/Drupal/Core/Entity/EntityDefinitionUpdateManager.php b/core/lib/Drupal/Core/Entity/EntityDefinitionUpdateManager.php
--- b/core/lib/Drupal/Core/Entity/EntityDefinitionUpdateManager.php
+++ b/core/lib/Drupal/Core/Entity/EntityDefinitionUpdateManager.php
@@ -130,7 +130,7 @@
               break;
 
             case static::DEFINITION_DELETED:
-              $this->entityManager->onFieldStorageDefinitionDelete($storage_definitions[$field_name]);
+              $this->entityManager->onFieldStorageDefinitionDelete($original_storage_definitions[$field_name]);
               break;
           }
         }
diff -u b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
--- b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
+++ b/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php
@@ -1673,6 +1673,13 @@
     }
     else {
       $data_table = $this->dataTable ?: $this->baseTable;
+      // @todo This check is here because system_system_info_alter() calls
+      //   countFieldData(), even in KernelTestBase tests, where the schema
+      //   might not have been created. Remove this when that function is
+      //   refactored. See that function for its issue links.
+      if (!$this->database->schema()->tableExists($data_table)) {
+        return $as_bool ? FALSE : 0;
+      }
       $query = $this->database->select($data_table, 't');
       $columns = $storage_definition->getColumns();
       if (count($columns) > 1) {
diff -u b/core/modules/system/system.module b/core/modules/system/system.module
--- b/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -8,7 +8,6 @@
 use Drupal\Component\Plugin\Exception\PluginNotFoundException;
 use Drupal\Core\Block\BlockPluginInterface;
 use Drupal\Core\Cache\Cache;
-use Drupal\Core\Entity\ContentEntityTypeInterface;
 use Drupal\Core\Extension\Extension;
 use Drupal\Core\Extension\ExtensionDiscovery;
 use Drupal\Core\Form\FormStateInterface;
@@ -1051,7 +1050,7 @@
           try {
             // We skip entity-defining modules, otherwise deleting all entities
             // would be required before being able to uninstall them.
-            if ($entity_type instanceof ContentEntityTypeInterface && $entity_type->getProvider() != $module_name) {
+            if ($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.