diff --git a/lib/DI/ContainerConfigurator.php b/lib/DI/ContainerConfigurator.php
index 99417788c8..e8a0313af9 100644
--- a/lib/DI/ContainerConfigurator.php
+++ b/lib/DI/ContainerConfigurator.php
@@ -268,6 +268,7 @@ class ContainerConfigurator implements IContainerConfigurator {
     $container->autowire(\MailPoet\Newsletter\NewslettersRepository::class)->setPublic(true);
     $container->autowire(\MailPoet\Newsletter\Listing\NewsletterListingRepository::class)->setPublic(true);
     $container->autowire(\MailPoet\Newsletter\Preview\SendPreviewController::class);
+    $container->autowire(\MailPoet\Newsletter\Segment\NewsletterSegmentRepository::class);
     $container->autowire(\MailPoet\Newsletter\Statistics\NewsletterStatisticsRepository::class);
     $container->autowire(\MailPoet\Newsletter\Scheduler\WelcomeScheduler::class)->setPublic(true);
     $container->autowire(\MailPoet\Newsletter\Scheduler\PostNotificationScheduler::class);
diff --git a/lib/Entities/NewsletterSegmentEntity.php b/lib/Entities/NewsletterSegmentEntity.php
index 5957a552f6..c925b2d65d 100644
--- a/lib/Entities/NewsletterSegmentEntity.php
+++ b/lib/Entities/NewsletterSegmentEntity.php
@@ -30,6 +30,11 @@ class NewsletterSegmentEntity {
    */
   private $segment;
 
+  public function __construct(NewsletterEntity $newsletter, SegmentEntity $segment) {
+    $this->newsletter = $newsletter;
+    $this->segment = $segment;
+  }
+
   /**
    * @return NewsletterEntity|null
    */
@@ -38,10 +43,6 @@ class NewsletterSegmentEntity {
     return $this->newsletter;
   }
 
-  public function setNewsletter(NewsletterEntity $newsletter) {
-    $this->newsletter = $newsletter;
-  }
-
   /**
    * @return SegmentEntity|null
    */
@@ -49,8 +50,4 @@ class NewsletterSegmentEntity {
     $this->safelyLoadToOneAssociation('segment');
     return $this->segment;
   }
-
-  public function setSegment(SegmentEntity $segment) {
-    $this->segment = $segment;
-  }
 }
diff --git a/lib/Newsletter/NewsletterSaveController.php b/lib/Newsletter/NewsletterSaveController.php
index b55696299d..18e9465b3d 100644
--- a/lib/Newsletter/NewsletterSaveController.php
+++ b/lib/Newsletter/NewsletterSaveController.php
@@ -4,14 +4,16 @@ namespace MailPoet\Newsletter;
 
 use MailPoet\Cron\Workers\SendingQueue\Tasks\Newsletter as NewsletterQueueTask;
 use MailPoet\Entities\NewsletterEntity;
+use MailPoet\Entities\NewsletterSegmentEntity;
+use MailPoet\Entities\SegmentEntity;
 use MailPoet\InvalidStateException;
 use MailPoet\Models\Newsletter;
 use MailPoet\Models\NewsletterOption;
 use MailPoet\Models\NewsletterOptionField;
-use MailPoet\Models\NewsletterSegment;
 use MailPoet\Models\SendingQueue;
 use MailPoet\Newsletter\Scheduler\PostNotificationScheduler;
 use MailPoet\Newsletter\Scheduler\Scheduler;
+use MailPoet\Newsletter\Segment\NewsletterSegmentRepository;
 use MailPoet\Newsletter\Url as NewsletterUrl;
 use MailPoet\NewsletterTemplates\NewsletterTemplatesRepository;
 use MailPoet\NotFoundException;
@@ -20,6 +22,7 @@ use MailPoet\Settings\SettingsController;
 use MailPoet\UnexpectedValueException;
 use MailPoet\WP\Emoji;
 use MailPoet\WP\Functions as WPFunctions;
+use MailPoetVendor\Doctrine\ORM\EntityManager;
 
 class NewsletterSaveController {
   /** @var AuthorizedEmailsController */
@@ -28,9 +31,15 @@ class NewsletterSaveController {
   /** @var Emoji */
   private $emoji;
 
+  /** @var EntityManager */
+  private $entityManager;
+
   /** @var NewslettersRepository */
   private $newslettersRepository;
 
+  /** @var NewsletterSegmentRepository */
+  private $newsletterSegmentRepository;
+
   /** @var NewsletterTemplatesRepository */
   private $newsletterTemplatesRepository;
 
@@ -46,7 +55,9 @@ class NewsletterSaveController {
   public function __construct(
     AuthorizedEmailsController $authorizedEmailsController,
     Emoji $emoji,
+    EntityManager $entityManager,
     NewslettersRepository $newslettersRepository,
+    NewsletterSegmentRepository $newsletterSegmentRepository,
     NewsletterTemplatesRepository $newsletterTemplatesRepository,
     PostNotificationScheduler $postNotificationScheduler,
     SettingsController $settings,
@@ -54,7 +65,9 @@ class NewsletterSaveController {
   ) {
     $this->authorizedEmailsController = $authorizedEmailsController;
     $this->emoji = $emoji;
+    $this->entityManager = $entityManager;
     $this->newslettersRepository = $newslettersRepository;
+    $this->newsletterSegmentRepository = $newsletterSegmentRepository;
     $this->newsletterTemplatesRepository = $newsletterTemplatesRepository;
     $this->postNotificationScheduler = $postNotificationScheduler;
     $this->settings = $settings;
@@ -83,6 +96,7 @@ class NewsletterSaveController {
 
     $newsletter = $this->getNewsletter($data);
     $this->updateNewsletter($newsletter, $data);
+    $this->updateSegments($newsletter, $data['segments'] ?? []);
 
     // fetch old model for back compatibility
     $newsletterModel = Newsletter::findOne((int)$data['id']);
@@ -90,19 +104,6 @@ class NewsletterSaveController {
       throw new InvalidStateException();
     }
 
-    $segments = $data['segments'] ?? [];
-    if ($segments) {
-      NewsletterSegment::where('newsletter_id', $newsletterModel->id)
-        ->deleteMany();
-      foreach ($segments as $segment) {
-        if (!is_array($segment)) continue;
-        $relation = NewsletterSegment::create();
-        $relation->segmentId = (int)$segment['id'];
-        $relation->newsletterId = $newsletterModel->id;
-        $relation->save();
-      }
-    }
-
     // save default sender if needed
     if (!$this->settings->get('sender') && !empty($data['sender_address']) && !empty($data['sender_name'])) {
       $this->settings->set('sender', [
@@ -221,4 +222,35 @@ class NewsletterSaveController {
 
     $this->newslettersRepository->flush();
   }
+
+  private function updateSegments(NewsletterEntity $newsletter, array $segments) {
+    $oldNewsletterSegments = $newsletter->getNewsletterSegments()->toArray();
+
+    // clear old & add new newsletter segments
+    $newsletter->getNewsletterSegments()->clear();
+    foreach ($segments as $segment) {
+      if (!is_array($segment) || !isset($segment['id'])) {
+        continue;
+      }
+
+      $segment = $this->entityManager->getReference(SegmentEntity::class, (int)$segment['id']);
+      $newsletterSegment = $this->newsletterSegmentRepository->findBy([
+        'newsletter' => $newsletter,
+        'segment' => $segment,
+      ]);
+
+      if (!$newsletterSegment) {
+        $newsletterSegment = new NewsletterSegmentEntity($newsletter, $segment);
+        $this->entityManager->persist($newsletterSegment);
+      }
+      $newsletter->getNewsletterSegments()->add($newsletterSegment);
+    }
+
+    // remove orphaned newsletter segments
+    foreach (array_diff($oldNewsletterSegments, $newsletter->getNewsletterSegments()->toArray()) as $newsletterSegment) {
+      $this->newsletterSegmentRepository->remove($newsletterSegment);
+    }
+
+    $this->entityManager->flush();
+  }
 }
diff --git a/lib/Newsletter/Segment/NewsletterSegmentRepository.php b/lib/Newsletter/Segment/NewsletterSegmentRepository.php
new file mode 100644
index 0000000000..4652f35409
--- /dev/null
+++ b/lib/Newsletter/Segment/NewsletterSegmentRepository.php
@@ -0,0 +1,15 @@
+<?php
+
+namespace MailPoet\Newsletter\Segment;
+
+use MailPoet\Doctrine\Repository;
+use MailPoet\Entities\NewsletterSegmentEntity;
+
+/**
+ * @extends Repository<NewsletterSegmentEntity>
+ */
+class NewsletterSegmentRepository extends Repository {
+  protected function getEntityClassName() {
+    return NewsletterSegmentEntity::class;
+  }
+}
diff --git a/tasks/phpstan/phpstan-baseline.neon b/tasks/phpstan/phpstan-baseline.neon
index 40126acbcb..bcad949f62 100644
--- a/tasks/phpstan/phpstan-baseline.neon
+++ b/tasks/phpstan/phpstan-baseline.neon
@@ -243,3 +243,8 @@ parameters:
 			message: "#^Parameter \\#1 \\$newsletter of method MailPoet\\\\Entities\\\\NewsletterTemplateEntity\\:\\:setNewsletter\\(\\) expects MailPoet\\\\Entities\\\\NewsletterEntity\\|null, object given\\.$#"
 			count: 1
 			path: ../../lib/NewsletterTemplates/NewsletterTemplatesRepository.php
+
+		-
+			message: "#^Parameter \\#2 \\$segment of class MailPoet\\\\Entities\\\\NewsletterSegmentEntity constructor expects MailPoet\\\\Entities\\\\SegmentEntity, object given\\.$#"
+			count: 1
+			path: ../../lib/Newsletter/NewsletterSaveController.php
diff --git a/tests/integration/Newsletter/Listing/NewsletterListingRepositoryTest.php b/tests/integration/Newsletter/Listing/NewsletterListingRepositoryTest.php
index 6c83f00ea3..7220b3779e 100644
--- a/tests/integration/Newsletter/Listing/NewsletterListingRepositoryTest.php
+++ b/tests/integration/Newsletter/Listing/NewsletterListingRepositoryTest.php
@@ -80,9 +80,7 @@ class NewsletterListingRepositoryTest extends \MailPoetTest {
     $newsletter->setSubject('Newsletter with segment');
     $this->entityManager->persist($newsletter);
 
-    $newsletterSegment = new NewsletterSegmentEntity();
-    $newsletterSegment->setSegment($segment);
-    $newsletterSegment->setNewsletter($newsletter);
+    $newsletterSegment = new NewsletterSegmentEntity($newsletter, $segment);
     $this->entityManager->persist($newsletterSegment);
 
     $this->entityManager->flush();