diff -u b/core/modules/color/src/Plugin/migrate/source/d7/Color.php b/core/modules/color/src/Plugin/migrate/source/d7/Color.php
--- b/core/modules/color/src/Plugin/migrate/source/d7/Color.php
+++ b/core/modules/color/src/Plugin/migrate/source/d7/Color.php
@@ -2,7 +2,12 @@
 
 namespace Drupal\color\Plugin\migrate\source\d7;
 
+use Drupal\Core\Extension\ThemeHandler;
 use Drupal\migrate_drupal\Plugin\migrate\source\VariableMultiRow;
+use Drupal\Core\Entity\EntityManagerInterface;
+use Drupal\Core\State\StateInterface;
+use Drupal\migrate\Plugin\MigrationInterface;
+use Symfony\Component\DependencyInjection\ContainerInterface;
 
 /**
  * Drupal 7 color source from database.
@@ -15,29 +20,60 @@
 class Color extends VariableMultiRow {
 
   /**
+   * The theme handler.
+   *
+   * @var \Drupal\Core\Extension\ThemeHandler
+   */
+  protected $themeHandler;
+
+  /**
+   * {@inheritdoc}
+   */
+  public function __construct(array $configuration, $plugin_id, $plugin_definition, MigrationInterface $migration, StateInterface $state, EntityManagerInterface $entity_manager, ThemeHandler $theme_handler) {
+    parent::__construct($configuration, $plugin_id, $plugin_definition, $migration, $state, $entity_manager);
+    $this->themeHandler = $theme_handler;
+  }
+
+  public static function create(ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition, MigrationInterface $migration = NULL) {
+    return new static(
+      $configuration,
+      $plugin_id,
+      $plugin_definition,
+      $migration,
+      $container->get('state'),
+      $container->get('entity.manager'),
+      $container->get('theme_handler')
+    );
+  }
+
+  /**
    * {@inheritdoc}
    */
   public function query() {
-    // Gets active themes.
-    $themes = $this->select('system', 's')
-      ->fields('s', ['name', 'type', 'status'])
-      ->condition('type', 'theme')
-      ->condition('status', '1')
-      ->execute()
-      ->fetchCol('name');
+     $themes = $this->themeHandler->listInfo();
+     $themes_installed = [];
+     /** @var \Drupal\Core\Extension\Extension $theme */
+    foreach($themes as $theme) {
+       if ($theme->status) {
+         $themes_installed[] = $theme->getName();
+       }
+     }
 
-    // Gets color data for active themes.
+    // Get color data for active themes.
     $query = $this->select('variable', 'v')
-      ->fields('v', ['name', 'value'])
-      // Screenshot is not in Drupal 8 configuration, exclude it here.
-      ->condition('name', 'color_%_screenshot', 'NOT LIKE');
-
-    $conditions = $query->orConditionGroup();
-    foreach ($themes as $theme) {
-      $active_theme = 'color_' . $theme . '_%';
-      $conditions->condition('name', $active_theme, 'LIKE');
+      ->fields('v', ['name', 'value']);
+
+    // Get all color variables for each active theme.
+    $or = $query->orConditionGroup();
+    foreach ($themes_installed as $theme) {
+      $variable_name = 'color_' . $theme . '_%';
+      $or->condition('name', $variable_name, 'LIKE');
     }
-    $query->condition($conditions);
+    // Screenshot is not in Drupal 8 configuration, exclude it here.
+    $condition = $query->andConditionGroup()
+      ->condition('name', 'color_%_screenshot', 'NOT LIKE')
+      ->condition($or);
+    $query->condition($condition);
     return $query;
   }
 
diff -u b/core/modules/color/tests/src/Kernel/Migrate/d7/MigrateColorTest.php b/core/modules/color/tests/src/Kernel/Migrate/d7/MigrateColorTest.php
--- b/core/modules/color/tests/src/Kernel/Migrate/d7/MigrateColorTest.php
+++ b/core/modules/color/tests/src/Kernel/Migrate/d7/MigrateColorTest.php
@@ -21,6 +21,8 @@
    */
   protected function setUp() {
     parent::setUp();
+    // Install the themes used for this test.
+    $this->container->get('theme_installer')->install(['bartik', 'classy', 'seven', 'stable', 'stark']);
     $this->executeMigration('d7_color');
   }
 
@@ -49,6 +51,9 @@
     ];
     $this->assertSame($palette, $config->get('palette'));
     $this->assertSame(['public://color/bartik-e0e23ad7/colors.css'], $config->get('stylesheets'));
+
+    // Test that garland was not migrated.
+    $this->assertEmpty(\Drupal::config('color.theme.garland')->get());
   }
 
 }
diff -u b/core/modules/color/tests/src/Kernel/Plugin/migrate/source/d7/ColorTest.php b/core/modules/color/tests/src/Kernel/Plugin/migrate/source/d7/ColorTest.php
--- b/core/modules/color/tests/src/Kernel/Plugin/migrate/source/d7/ColorTest.php
+++ b/core/modules/color/tests/src/Kernel/Plugin/migrate/source/d7/ColorTest.php
@@ -59,12 +59,29 @@
         'name' => 'color_bartik_screenshot',
         'value' => ['public:://color/bartik-b69cfcec/screenshot.png'],
       ],
+      [
+        'name' => 'color_custom_stylesheets',
+        'value' => ['public:://color/custom-beadedff/screenshot.png'],
+      ],
     ];
 
     foreach ($tests[0]['database']['variable'] as $key => $expected) {
       $tests[0]['database']['variable'][$key]['value'] = serialize($expected['value']);
     }
 
+    $tests[0]['database']['system'] = [
+      [
+        'name' => 'bartik',
+        'type' => 'theme',
+        'status' => '1',
+      ],
+      [
+        'name' => 'custom',
+        'type' => 'theme',
+        'status' => '0',
+      ],
+    ];
+
     $tests[0]['expected_results'] = [
       [
         'name' => 'color_bartik_palette',
@@ -96,6 +113,7 @@
         ],
       ],
     ];
+
     return $tests;
   }