diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12c68daa..921e45d4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,6 +34,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com), and this
 ### Changed
 * [#1339](https://github.com/shlinkio/shlink/issues/1339) Added new test suite for CLI E2E tests.
 * [#1503](https://github.com/shlinkio/shlink/issues/1503) Drastically improved build time in GitHub Actions, by optimizing parallelization, adding php extensions cache and running mutation tests only for changed files.
+* [#1525](https://github.com/shlinkio/shlink/issues/1525) Migrated to custom doctrine CLI entry point.
 
 ### Deprecated
 * *Nothing*
diff --git a/bin/doctrine b/bin/doctrine
new file mode 100755
index 00000000..4fec1714
--- /dev/null
+++ b/bin/doctrine
@@ -0,0 +1,12 @@
+#!/usr/bin/env php
+<?php
+
+declare(strict_types=1);
+
+use Doctrine\ORM\EntityManager;
+use Doctrine\ORM\Tools\Console\ConsoleRunner;
+use Doctrine\ORM\Tools\Console\EntityManagerProvider\SingleManagerProvider;
+
+/** @var EntityManager $app */
+$em = require __DIR__ . '/../config/entity-manager.php';
+ConsoleRunner::run(new SingleManagerProvider($em));
diff --git a/composer.json b/composer.json
index 99e6cb21..a9b60f12 100644
--- a/composer.json
+++ b/composer.json
@@ -71,7 +71,7 @@
         "phpunit/phpunit": "^9.5",
         "roave/security-advisories": "dev-master",
         "shlinkio/php-coding-standard": "~2.3.0",
-        "shlinkio/shlink-test-utils": "^3.2",
+        "shlinkio/shlink-test-utils": "dev-main#404fdf6 as 3.3",
         "symfony/var-dumper": "^6.1",
         "veewee/composer-run-parallel": "^1.1"
     },
diff --git a/config/autoload/installer.global.php b/config/autoload/installer.global.php
index a7a4c97a..40c2f4bd 100644
--- a/config/autoload/installer.global.php
+++ b/config/autoload/installer.global.php
@@ -73,6 +73,12 @@ return [
             InstallationCommand::DB_MIGRATE->value => [
                 'command' => 'bin/cli ' . Command\Db\MigrateDatabaseCommand::NAME,
             ],
+            InstallationCommand::ORM_PROXIES->value => [
+                'command' => 'bin/doctrine orm:generate-proxies',
+            ],
+            InstallationCommand::ORM_CLEAR_CACHE->value => [
+                'command' => 'bin/doctrine orm:clear-cache:metadata',
+            ],
             InstallationCommand::GEOLITE_DOWNLOAD_DB->value => [
                 'command' => 'bin/cli ' . Command\Visit\DownloadGeoLiteDbCommand::NAME,
             ],
diff --git a/config/test/bootstrap_api_tests.php b/config/test/bootstrap_api_tests.php
index bc119284..2653b552 100644
--- a/config/test/bootstrap_api_tests.php
+++ b/config/test/bootstrap_api_tests.php
@@ -28,6 +28,11 @@ register_shutdown_function(function () use ($httpClient): void {
     );
 });
 
-$testHelper->createTestDb(['bin/cli', 'db:create'], ['bin/cli', 'db:migrate']);
+$testHelper->createTestDb(
+    ['bin/cli', 'db:create'],
+    ['bin/cli', 'db:migrate'],
+    ['bin/doctrine', 'orm:schema-tool:drop'],
+    ['bin/doctrine', 'dbal:run-sql'],
+);
 ApiTest\ApiTestCase::setApiClient($httpClient);
 ApiTest\ApiTestCase::setSeedFixturesCallback(fn () => $testHelper->seedFixtures($em, $config['data_fixtures'] ?? []));
diff --git a/config/test/bootstrap_cli_tests.php b/config/test/bootstrap_cli_tests.php
index 893bdfd7..c8c33721 100644
--- a/config/test/bootstrap_cli_tests.php
+++ b/config/test/bootstrap_cli_tests.php
@@ -22,7 +22,12 @@ if (file_exists($covFile)) {
     unlink($covFile);
 }
 
-$testHelper->createTestDb(['bin/cli', 'db:create'], ['bin/cli', 'db:migrate']);
+$testHelper->createTestDb(
+    ['bin/cli', 'db:create'],
+    ['bin/cli', 'db:migrate'],
+    ['bin/doctrine', 'orm:schema-tool:drop'],
+    ['bin/doctrine', 'dbal:run-sql'],
+);
 CliTest\CliTestCase::setSeedFixturesCallback(
     static fn () => $testHelper->seedFixtures($em, $config['data_fixtures'] ?? []),
 );
diff --git a/config/test/bootstrap_db_tests.php b/config/test/bootstrap_db_tests.php
index 0237d741..5aa8ea51 100644
--- a/config/test/bootstrap_db_tests.php
+++ b/config/test/bootstrap_db_tests.php
@@ -8,5 +8,10 @@ use Psr\Container\ContainerInterface;
 
 /** @var ContainerInterface $container */
 $container = require __DIR__ . '/../container.php';
-$container->get(Helper\TestHelper::class)->createTestDb(['bin/cli', 'db:create'], ['bin/cli', 'db:migrate']);
+$container->get(Helper\TestHelper::class)->createTestDb(
+    ['bin/cli', 'db:create'],
+    ['bin/cli', 'db:migrate'],
+    ['bin/doctrine', 'orm:schema-tool:drop'],
+    ['bin/doctrine', 'dbal:run-sql'],
+);
 DbTest\DatabaseTestCase::setEntityManager($container->get('em'));
diff --git a/docker/docker-entrypoint.sh b/docker/docker-entrypoint.sh
index 1955f0ec..f28627d2 100644
--- a/docker/docker-entrypoint.sh
+++ b/docker/docker-entrypoint.sh
@@ -13,10 +13,10 @@ echo "Updating database..."
 php bin/cli db:migrate -n ${flags}
 
 echo "Generating proxies..."
-php vendor/doctrine/orm/bin/doctrine.php orm:generate-proxies -n ${flags}
+php bin/doctrine orm:generate-proxies -n ${flags}
 
 echo "Clearing entities cache..."
-php vendor/doctrine/orm/bin/doctrine.php orm:clear-cache:metadata -n ${flags}
+php bin/doctrine orm:clear-cache:metadata -n ${flags}
 
 # Try to download GeoLite2 db file only if the license key env var was defined
 if [ ! -z "${GEOLITE_LICENSE_KEY}" ]; then
diff --git a/module/CLI/src/Command/Db/CreateDatabaseCommand.php b/module/CLI/src/Command/Db/CreateDatabaseCommand.php
index 415290a3..5cc6a184 100644
--- a/module/CLI/src/Command/Db/CreateDatabaseCommand.php
+++ b/module/CLI/src/Command/Db/CreateDatabaseCommand.php
@@ -22,7 +22,7 @@ use const Shlinkio\Shlink\MIGRATIONS_TABLE;
 class CreateDatabaseCommand extends AbstractDatabaseCommand
 {
     public const NAME = 'db:create';
-    public const DOCTRINE_SCRIPT = 'vendor/doctrine/orm/bin/doctrine.php';
+    public const DOCTRINE_SCRIPT = 'bin/doctrine';
     public const DOCTRINE_CREATE_SCHEMA_COMMAND = 'orm:schema-tool:create';
 
     public function __construct(