diff -u b/core/modules/migrate/src/MigrateExecutable.php b/core/modules/migrate/src/MigrateExecutable.php
--- b/core/modules/migrate/src/MigrateExecutable.php
+++ b/core/modules/migrate/src/MigrateExecutable.php
@@ -387,8 +387,13 @@
         }
       }
       // No plugins or no value means do not set.
-      if ($plugins && !is_null($value)) {
-        $row->setDestinationProperty($destination, $value);
+      if ($plugins) {
+        if (isset($value)) {
+          $row->setDestinationProperty($destination, $value);
+        }
+        else {
+          $row->setEmptyDestinationProperty($destination);
+        }
       }
       // Reset the value.
       $value = NULL;
@@ -402,13 +407,8 @@
         }
       }
       // No plugins or no value means do not set.
-      if ($plugins) {
-        if (isset($value)) {
-          $row->setDestinationProperty($destination, $value);
-        }
-        else {
-          $row->setEmptyDestinationProperty($destination);
-        }
+      if ($plugins && !is_null($value)) {
+        $row->setDestinationProperty($destination, $value);
       }
       // Reset the value.
       $value = NULL;
diff -u b/core/modules/migrate/tests/src/Kernel/MigrateEntityContentBaseTest.php b/core/modules/migrate/tests/src/Kernel/MigrateEntityContentBaseTest.php
--- b/core/modules/migrate/tests/src/Kernel/MigrateEntityContentBaseTest.php
+++ b/core/modules/migrate/tests/src/Kernel/MigrateEntityContentBaseTest.php
@@ -160,9 +160,9 @@
   }
 
   /**
-   * Tests empty destinations.
+   * Tests creation of ID columns table with definitions taken from entity type.
    */
-  public function testEmptyDestinations() {
+  public function testEntityWithStringId() {
     $this->enableModules(['migrate_entity_test']);
     $this->installEntitySchema('migrate_string_id_entity_test');
 
@@ -180,7 +180,6 @@
           'id' => ['type' => 'integer', 'size' => 'big'],
           'version' => ['type' => 'string'],
         ],
-        'constants' => ['null' => NULL],
       ],
       'process' => [
         'id' => 'id',
@@ -191,6 +190,53 @@
       ],
     ];
 
+    $migration = \Drupal::service('plugin.manager.migration')->createStubMigration($definition);
+    $executable = new MigrateExecutable($migration, new MigrateMessage());
+    $result = $executable->import();
+    $this->assertEquals(MigrationInterface::RESULT_COMPLETED, $result);
+
+    /** @var \Drupal\migrate\Plugin\MigrateIdMapInterface $id_map_plugin */
+    $id_map_plugin = $migration->getIdMap();
+
+    // Check that the destination has been stored.
+    $map_row = $id_map_plugin->getRowBySource(['id' => 123, 'version' => 'foo']);
+    $this->assertEquals(123, $map_row['destid1']);
+    $map_row = $id_map_plugin->getRowBySource(['id' => 123456789012, 'version' => 'bar']);
+    $this->assertEquals(123456789012, $map_row['destid1']);
+  }
+
+  /**
+   * Tests empty destinations.
+   */
+  public function testEmptyDestinations() {
+    $this->enableModules(['migrate_entity_test']);
+    $this->installEntitySchema('migrate_string_id_entity_test');
+
+    $definition = [
+      'source' => [
+        'plugin' => 'embedded_data',
+        'data_rows' => [
+          ['id' => 123, 'version' => 'foo'],
+          // This integer needs an 'int' schema with 'big' size. If 'destid1'
+          // is not correctly taking the definition from the destination entity
+          // type, the import will fail with a SQL exception.
+          ['id' => 123456789012, 'version' => 'bar'],
+        ],
+        'ids' => [
+          'id' => ['type' => 'integer', 'size' => 'big'],
+          'version' => ['type' => 'string'],
+        ],
+        'constants' => ['null' => NULL],
+      ],
+      'process' => [
+        'id' => 'id',
+        'version' => 'version',
+      ],
+      'destination' => [
+        'plugin' => 'entity:migrate_string_id_entity_test',
+      ],
+    ];
+
     $migration = \Drupal::service('plugin.manager.migration')
       ->createStubMigration($definition);
     $executable = new MigrateExecutable($migration, new MigrateMessage());