diff -u b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
--- b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
+++ b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
@@ -122,8 +122,10 @@
       $this->updateEntity($entity, $row);
     }
     else {
-      if ($bundle = $this->getEntityBundleId()) {
-        $row->setDestinationProperty($this->getKey('bundle'), $bundle);
+      $bundle_key = $this->getKey('bundle');
+      // Apply any configured bundle if the bundle has not already been set.
+      if (($bundle = $this->getEntityBundleId()) && empty($row->getDestinationProperty($bundle_key))) {
+        $row->setDestinationProperty($bundle_key, $bundle);
       }
 
       // Stubs might need some required fields filled in.
only in patch2:
unchanged:
--- /dev/null
+++ b/core/modules/migrate/tests/src/Kernel/MigrateBundleTest.php
@@ -0,0 +1,155 @@
+<?php
+
+namespace Drupal\Tests\migrate\Kernel;
+
+use Drupal\migrate\MigrateExecutable;
+use Drupal\taxonomy\Entity\Term;
+use Drupal\taxonomy\Entity\Vocabulary;
+
+/**
+ * Tests setting of bundles on content entity migrations.
+ *
+ * @group migrate
+ */
+class MigrateBundleTest extends MigrateTestBase {
+
+  /**
+   * Modules to enable.
+   *
+   * @var array
+   */
+  public static $modules = ['field', 'taxonomy', 'text'];
+
+  /**
+   * {@inheritdoc}
+   */
+  protected function setUp() {
+    parent::setUp();
+    $this->installEntitySchema('taxonomy_vocabulary');
+    $this->installEntitySchema('taxonomy_term');
+    $this->installConfig(['taxonomy']);
+    // Set up two vocabularies (taxonomy bundles).
+    Vocabulary::create(['vid' => 'tags', 'name' => 'Tags']);
+    Vocabulary::create(['vid' => 'categories', 'name' => 'Categories']);
+  }
+
+  /**
+   * Tests setting the bundle in the destination.
+   */
+  public function testDestinationBundle() {
+    $term_data_rows = [
+      ['id' => 1, 'name' => 'Category 1'],
+    ];
+    $ids = ['id' => ['type' => 'integer']];
+    $definition = [
+      'id' => 'terms',
+      'migration_tags' => ['Bundle test'],
+      'source' => [
+        'plugin' => 'embedded_data',
+        'data_rows' => $term_data_rows,
+        'ids' => $ids,
+      ],
+      'process' => [
+        'tid' => 'id',
+        'name' => 'name',
+      ],
+      'destination' => [
+        'plugin' => 'entity:taxonomy_term',
+        'bundle' => 'categories',
+      ],
+      'migration_dependencies' => [],
+    ];
+
+    $term_migration = \Drupal::service('plugin.manager.migration')->createStubMigration($definition);
+
+    // Import and validate the term entity was created with the correct bundle.
+    $term_executable = new MigrateExecutable($term_migration, $this);
+    $term_executable->import();
+    /** @var Term $term */
+    $term = Term::load(1);
+    $this->assertEquals($term->bundle(), 'categories');
+  }
+
+  /**
+   * Tests setting the bundle in the process pipeline.
+   */
+  public function testProcessBundle() {
+    $term_data_rows = [
+      ['id' => 1, 'vocab' => 'categories', 'name' => 'Category 1'],
+      ['id' => 2, 'vocab' => 'tags', 'name' => 'Tag 1'],
+    ];
+    $ids = ['id' => ['type' => 'integer']];
+    $definition = [
+      'id' => 'terms',
+      'migration_tags' => ['Bundle test'],
+      'source' => [
+        'plugin' => 'embedded_data',
+        'data_rows' => $term_data_rows,
+        'ids' => $ids,
+      ],
+      'process' => [
+        'tid' => 'id',
+        'vid' => 'vocab',
+        'name' => 'name',
+      ],
+      'destination' => [
+        'plugin' => 'entity:taxonomy_term',
+      ],
+      'migration_dependencies' => [],
+    ];
+
+    $term_migration = \Drupal::service('plugin.manager.migration')->createStubMigration($definition);
+
+    // Import and validate the term entities were created with the correct bundle.
+    $term_executable = new MigrateExecutable($term_migration, $this);
+    $term_executable->import();
+    /** @var Term $term */
+    $term = Term::load(1);
+    $this->assertEquals($term->bundle(), 'categories');
+    $term = Term::load(2);
+    $this->assertEquals($term->bundle(), 'tags');
+  }
+
+  /**
+   * Tests setting bundles both in process and destination.
+   */
+  public function testMixedBundles() {
+    $term_data_rows = [
+      ['id' => 1, 'vocab' => 'categories', 'name' => 'Category 1'],
+      ['id' => 2, 'name' => 'Tag 1'],
+    ];
+    $ids = ['id' => ['type' => 'integer']];
+    $definition = [
+      'id' => 'terms',
+      'migration_tags' => ['Bundle test'],
+      'source' => [
+        'plugin' => 'embedded_data',
+        'data_rows' => $term_data_rows,
+        'ids' => $ids,
+      ],
+      'process' => [
+        'tid' => 'id',
+        'vid' => 'vocab',
+        'name' => 'name',
+      ],
+      'destination' => [
+        'plugin' => 'entity:taxonomy_term',
+        // When no vocab is provided, the destination bundle is applied.
+        'bundle' => 'tags',
+      ],
+      'migration_dependencies' => [],
+    ];
+
+    $term_migration = \Drupal::service('plugin.manager.migration')->createStubMigration($definition);
+
+    // Import and validate the term entities were created with the correct bundle.
+    $term_executable = new MigrateExecutable($term_migration, $this);
+    $term_executable->import();
+    /** @var Term $term */
+    $term = Term::load(1);
+    $this->assertEquals($term->bundle(), 'categories');
+    $term = Term::load(2);
+    $this->assertEquals($term->bundle(), 'tags');
+  }
+
+}