diff --git a/django/core/management/commands/migrate.py b/django/core/management/commands/migrate.py
index 1541843066c..3a0e9e87ff8 100644
--- a/django/core/management/commands/migrate.py
+++ b/django/core/management/commands/migrate.py
@@ -195,8 +195,11 @@ class Command(BaseCommand):
                 )
             if self.verbosity > 0:
                 self.stdout.write("Pruning migrations:", self.style.MIGRATE_HEADING)
-            to_prune = set(executor.loader.applied_migrations) - set(
-                executor.loader.disk_migrations
+            to_prune = sorted(
+                migration
+                for migration in set(executor.loader.applied_migrations)
+                - set(executor.loader.disk_migrations)
+                if migration[0] == app_label
             )
             squashed_migrations_with_deleted_replaced_migrations = [
                 migration_key
@@ -222,9 +225,6 @@ class Command(BaseCommand):
                     )
                 )
             else:
-                to_prune = sorted(
-                    migration for migration in to_prune if migration[0] == app_label
-                )
                 if to_prune:
                     for migration in to_prune:
                         app, name = migration
diff --git a/tests/migrations/test_commands.py b/tests/migrations/test_commands.py
index 1f8b3fb0114..6ef172ee6fa 100644
--- a/tests/migrations/test_commands.py
+++ b/tests/migrations/test_commands.py
@@ -1427,6 +1427,53 @@ class MigrateTests(MigrationTestBase):
         with self.assertRaisesMessage(CommandError, msg):
             call_command("migrate", prune=True)
 
+    @override_settings(
+        MIGRATION_MODULES={
+            "migrations": "migrations.test_migrations_squashed_no_replaces",
+            "migrations2": "migrations2.test_migrations_2_squashed_with_replaces",
+        },
+        INSTALLED_APPS=["migrations", "migrations2"],
+    )
+    def test_prune_respect_app_label(self):
+        recorder = MigrationRecorder(connection)
+        recorder.record_applied("migrations", "0001_initial")
+        recorder.record_applied("migrations", "0002_second")
+        recorder.record_applied("migrations", "0001_squashed_0002")
+        # Second app has squashed migrations with replaces.
+        recorder.record_applied("migrations2", "0001_initial")
+        recorder.record_applied("migrations2", "0002_second")
+        recorder.record_applied("migrations2", "0001_squashed_0002")
+        out = io.StringIO()
+        try:
+            call_command("migrate", "migrations", prune=True, stdout=out, no_color=True)
+            self.assertEqual(
+                out.getvalue(),
+                "Pruning migrations:\n"
+                "  Pruning migrations.0001_initial OK\n"
+                "  Pruning migrations.0002_second OK\n",
+            )
+            applied_migrations = [
+                migration
+                for migration in recorder.applied_migrations()
+                if migration[0] in ["migrations", "migrations2"]
+            ]
+            self.assertEqual(
+                applied_migrations,
+                [
+                    ("migrations", "0001_squashed_0002"),
+                    ("migrations2", "0001_initial"),
+                    ("migrations2", "0002_second"),
+                    ("migrations2", "0001_squashed_0002"),
+                ],
+            )
+        finally:
+            recorder.record_unapplied("migrations", "0001_initial")
+            recorder.record_unapplied("migrations", "0001_second")
+            recorder.record_unapplied("migrations", "0001_squashed_0002")
+            recorder.record_unapplied("migrations2", "0001_initial")
+            recorder.record_unapplied("migrations2", "0002_second")
+            recorder.record_unapplied("migrations2", "0001_squashed_0002")
+
 
 class MakeMigrationsTests(MigrationTestBase):
     """
diff --git a/tests/migrations2/test_migrations_2_squashed_with_replaces/0001_squashed_0002.py b/tests/migrations2/test_migrations_2_squashed_with_replaces/0001_squashed_0002.py
new file mode 100644
index 00000000000..30700e5eb6e
--- /dev/null
+++ b/tests/migrations2/test_migrations_2_squashed_with_replaces/0001_squashed_0002.py
@@ -0,0 +1,30 @@
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    replaces = [
+        ("migrations2", "0001_initial"),
+        ("migrations2", "0002_second"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            "OtherAuthor",
+            [
+                ("id", models.AutoField(primary_key=True)),
+                ("name", models.CharField(max_length=255)),
+            ],
+        ),
+        migrations.CreateModel(
+            "OtherBook",
+            [
+                ("id", models.AutoField(primary_key=True)),
+                (
+                    "author",
+                    models.ForeignKey(
+                        "migrations2.OtherAuthor", models.SET_NULL, null=True
+                    ),
+                ),
+            ],
+        ),
+    ]
diff --git a/tests/migrations2/test_migrations_2_squashed_with_replaces/__init__.py b/tests/migrations2/test_migrations_2_squashed_with_replaces/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d