diff --git a/UPGRADE.md b/UPGRADE.md
index aa5f20b19d6..3e453d7d78c 100644
--- a/UPGRADE.md
+++ b/UPGRADE.md
@@ -1,5 +1,13 @@
 # Upgrade to 2.12
 
+## Deprecated the `doctrine` binary.
+
+The documentation explains how the console tools can be bootstrapped for
+standalone usage.
+
+The method `ConsoleRunner::printCliConfigTemplate()` is deprecated because it
+was only useful in the context of the `doctrine` binary.
+
 ## Deprecate omitting `$class` argument to `ORMInvalidArgumentException::invalidIdentifierBindingEntity()`
 
 To make it easier to identify understand the cause for that exception, it is
@@ -13,6 +21,7 @@ multiple entity managers had been deprecated with 2.9 already. This leaves
 The `EntityManagerHelper` class with no purpose which is why it is now
 deprecated too. Applications that still rely on the `em` console helper, can
 easily recreate that class in their own codebase.
+
 ## Deprecate custom repository classes that don't extend `EntityRepository`
 
 Although undocumented, it is currently possible to configure a custom repository
diff --git a/bin/doctrine-pear.php b/bin/doctrine-pear.php
index 4ac3f0015d9..85cb067667a 100644
--- a/bin/doctrine-pear.php
+++ b/bin/doctrine-pear.php
@@ -1,5 +1,14 @@
 <?php
 
+fwrite(
+    STDERR,
+    '[Warning] The use of this script is discouraged.'
+    . ' You find instructions on how to boostrap the console runner in our documentation.'
+    . PHP_EOL
+);
+
+echo PHP_EOL . PHP_EOL;
+
 require_once 'Doctrine/Common/ClassLoader.php';
 
 $classLoader = new \Doctrine\Common\ClassLoader('Doctrine');
diff --git a/bin/doctrine.php b/bin/doctrine.php
index 9e89c2044e0..d2e1c3253f3 100644
--- a/bin/doctrine.php
+++ b/bin/doctrine.php
@@ -3,6 +3,15 @@
 use Symfony\Component\Console\Helper\HelperSet;
 use Doctrine\ORM\Tools\Console\ConsoleRunner;
 
+fwrite(
+    STDERR,
+    '[Warning] The use of this script is discouraged.'
+    . ' You find instructions on how to boostrap the console runner in our documentation.'
+    . PHP_EOL
+);
+
+echo PHP_EOL . PHP_EOL;
+
 $autoloadFiles = [
     __DIR__ . '/../vendor/autoload.php',
     __DIR__ . '/../../../autoload.php'
diff --git a/docs/en/reference/advanced-configuration.rst b/docs/en/reference/advanced-configuration.rst
index 82e4a5b6cad..70a4fb358e5 100644
--- a/docs/en/reference/advanced-configuration.rst
+++ b/docs/en/reference/advanced-configuration.rst
@@ -457,17 +457,5 @@ Setting up the Console
 ----------------------
 
 Doctrine uses the Symfony Console component for generating the command
-line interface. You can take a look at the ``vendor/bin/doctrine.php``
-script and the ``Doctrine\ORM\Tools\Console\ConsoleRunner`` command
-for inspiration how to setup the cli.
-
-In general the required code looks like this:
-
-.. code-block:: php
-
-    <?php
-    $cli = new Application('Doctrine Command Line Interface', \Doctrine\ORM\Version::VERSION);
-    $cli->setCatchExceptions(true);
-    $cli->setHelperSet($helperSet);
-    Doctrine\ORM\Tools\Console\ConsoleRunner::addCommands($cli);
-    $cli->run();
+line interface. You can take a look at the
+:doc:`tools chapter <../reference/tools>` for inspiration how to setup the cli.
diff --git a/docs/en/reference/configuration.rst b/docs/en/reference/configuration.rst
index 03a520ce8cb..47b0366a963 100644
--- a/docs/en/reference/configuration.rst
+++ b/docs/en/reference/configuration.rst
@@ -111,26 +111,6 @@ Setting up the Commandline Tool
 -------------------------------
 
 Doctrine ships with a number of command line tools that are very helpful
-during development. You can call this command from the Composer binary
-directory:
-
-.. code-block:: sh
-
-    $ php vendor/bin/doctrine
-
-You need to register your applications EntityManager to the console tool
-to make use of the tasks by creating a ``cli-config.php`` file with the
-following content:
-
-.. code-block:: php
-
-    <?php
-    use Doctrine\ORM\Tools\Console\ConsoleRunner;
-
-    // replace with file to your own project bootstrap
-    require_once 'bootstrap.php';
-
-    // replace with mechanism to retrieve EntityManager in your app
-    $entityManager = GetEntityManager();
-
-    return ConsoleRunner::createHelperSet($entityManager);
+during development. In order to make use of them, create an executable PHP
+script in your project as described in the
+:doc:`tools chapter <../reference/tools>`.
diff --git a/docs/en/reference/tools.rst b/docs/en/reference/tools.rst
index f42b35ac0d2..eb9631695fe 100644
--- a/docs/en/reference/tools.rst
+++ b/docs/en/reference/tools.rst
@@ -7,24 +7,10 @@ Doctrine Console
 The Doctrine Console is a Command Line Interface tool for simplifying common
 administration tasks during the development of a project that uses ORM.
 
-Take a look at the :doc:`Installation and Configuration <configuration>`
-chapter for more information how to setup the console command.
+For the following examples, we will set up the CLI as ``bin/doctrine``.
 
-Display Help Information
-~~~~~~~~~~~~~~~~~~~~~~~~
-
-Type ``php vendor/bin/doctrine`` on the command line and you should see an
-overview of the available commands or use the --help flag to get
-information on the available commands. If you want to know more
-about the use of generate entities for example, you can call:
-
-.. code-block:: php
-
-    $> php vendor/bin/doctrine orm:generate-entities --help
-
-
-Configuration
-~~~~~~~~~~~~~
+Setting Up the Console
+~~~~~~~~~~~~~~~~~~~~~~
 
 Whenever the ``doctrine`` command line tool is invoked, it can
 access all Commands that were registered by a developer. There is no
@@ -34,25 +20,33 @@ Doctrine DBAL and ORM. If you want to use additional commands you
 have to register them yourself.
 
 All the commands of the Doctrine Console require access to the
-``EntityManager``. You have to inject it into the console application with
-``ConsoleRunner::createHelperSet``. Whenever you invoke the Doctrine
-binary, it searches the current directory for the file ``cli-config.php``.
-This file contains the project-specific configuration.
+``EntityManager``. You have to inject it into the console application.
 
-Here is an example of a the project-specific ``cli-config.php``:
+Here is an example of a the project-specific ``bin/doctrine`` binary.
 
 .. code-block:: php
 
+    #!/usr/bin/env php
     <?php
+
     use Doctrine\ORM\Tools\Console\ConsoleRunner;
+    use Doctrine\ORM\Tools\Console\EntityManagerProvider\SingleManagerProvider;
 
-    // replace this with the path to your own project bootstrap file.
+    // replace with file to your own project bootstrap
     require_once 'bootstrap.php';
 
     // replace with mechanism to retrieve EntityManager in your app
     $entityManager = GetEntityManager();
 
-    return ConsoleRunner::createHelperSet($entityManager);
+    $commands = [
+        // If you want to add your own custom console commands,
+        // you can do so here.
+    ];
+
+    ConsoleRunner::run(
+        new SingleManagerProvider($entityManager),
+        $commands
+    );
 
 .. note::
 
@@ -60,6 +54,18 @@ Here is an example of a the project-specific ``cli-config.php``:
     and use their facilities to access the Doctrine EntityManager and
     Connection Resources.
 
+Display Help Information
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Type ``php bin/doctrine`` on the command line and you should see an
+overview of the available commands or use the --help flag to get
+information on the available commands. If you want to know more
+about the use of generate entities for example, you can call:
+
+::
+
+    $> php bin/doctrine orm:generate-entities --help
+
 Command Overview
 ~~~~~~~~~~~~~~~~
 
@@ -189,38 +195,35 @@ To create the schema use the ``create`` command:
 
 .. code-block:: php
 
-    $ php doctrine orm:schema-tool:create
+    $ php bin/doctrine orm:schema-tool:create
 
 To drop the schema use the ``drop`` command:
 
 .. code-block:: php
 
-    $ php doctrine orm:schema-tool:drop
+    $ php bin/doctrine orm:schema-tool:drop
 
 If you want to drop and then recreate the schema then use both
 options:
 
 .. code-block:: php
 
-    $ php doctrine orm:schema-tool:drop
-    $ php doctrine orm:schema-tool:create
+    $ php bin/doctrine orm:schema-tool:drop
+    $ php bin/doctrine orm:schema-tool:create
 
 As you would think, if you want to update your schema use the
 ``update`` command:
 
 .. code-block:: php
 
-    $ php doctrine orm:schema-tool:update
+    $ php bin/doctrine orm:schema-tool:update
 
 All of the above commands also accept a ``--dump-sql`` option that
 will output the SQL for the ran operation.
 
 .. code-block:: php
 
-    $ php doctrine orm:schema-tool:create --dump-sql
-
-Before using the orm:schema-tool commands, remember to configure
-your cli-config.php properly.
+    $ php bin/doctrine orm:schema-tool:create --dump-sql
 
 Entity Generation
 -----------------
@@ -229,9 +232,9 @@ Generate entity classes and method stubs from your mapping information.
 
 .. code-block:: php
 
-    $ php doctrine orm:generate-entities
-    $ php doctrine orm:generate-entities --update-entities
-    $ php doctrine orm:generate-entities --regenerate-entities
+    $ php bin/doctrine orm:generate-entities
+    $ php bin/doctrine orm:generate-entities --update-entities
+    $ php bin/doctrine orm:generate-entities --regenerate-entities
 
 This command is not suited for constant usage. It is a little helper and does
 not support all the mapping edge cases very well. You still have to put work
@@ -316,7 +319,7 @@ convert to and the path to generate it:
 
 .. code-block:: php
 
-    $ php doctrine orm:convert-mapping xml /path/to/mapping-path-converted-to-xml
+    $ php bin/doctrine orm:convert-mapping xml /path/to/mapping-path-converted-to-xml
 
 Reverse Engineering
 -------------------
@@ -366,7 +369,7 @@ You can also reverse engineer a database using the
 
 .. code-block:: php
 
-    $ php doctrine orm:convert-mapping --from-database yml /path/to/mapping-path-converted-to-yml
+    $ php bin/doctrine orm:convert-mapping --from-database yml /path/to/mapping-path-converted-to-yml
 
 .. note::
 
diff --git a/docs/en/tutorials/getting-started.rst b/docs/en/tutorials/getting-started.rst
index d96a8c5f768..a9200997dd3 100644
--- a/docs/en/tutorials/getting-started.rst
+++ b/docs/en/tutorials/getting-started.rst
@@ -191,22 +191,35 @@ Generating the Database Schema
 
 Doctrine has a command-line interface that allows you to access the SchemaTool,
 a component that can generate a relational database schema based entirely on the
-defined entity classes and their metadata. For this tool to work, a
-``cli-config.php`` file must exist in the project root directory:
+defined entity classes and their metadata. For this tool to work, you need to
+create an executable console script as described in the
+:doc:`tools chapter <../reference/tools>`.
+
+If you created the ``bootstrap.php`` file as described in the previous section,
+that script could look like this:
 
 .. code-block:: php
 
+    #!/usr/bin/env php
     <?php
-    // cli-config.php
-    require_once "bootstrap.php";
+    // bin/doctrine
+
+    use Doctrine\ORM\Tools\Console\ConsoleRunner;
+    use Doctrine\ORM\Tools\Console\EntityManagerProvider\SingleManagerProvider;
 
-    return \Doctrine\ORM\Tools\Console\ConsoleRunner::createHelperSet($entityManager);
+    // Adjust this path to your actual bootstrap.php
+    require __DIR__ . 'path/to/your/bootstrap.php';
+
+    ConsoleRunner::run(
+        new SingleManagerProvider($entityManager)
+    );
 
-Now call the Doctrine command-line tool:
+In the following examples, we will assume that this script has been created as
+``bin/doctrine``.
 
 ::
 
-    $ vendor/bin/doctrine orm:schema-tool:create
+    $ php bin/doctrine orm:schema-tool:create
 
 Since we haven't added any entity metadata in ``src`` yet, you'll see a message
 stating "No Metadata Classes to process." In the next section, we'll create a
@@ -218,14 +231,14 @@ You can easily recreate the database using the following commands:
 
 ::
 
-    $ vendor/bin/doctrine orm:schema-tool:drop --force
-    $ vendor/bin/doctrine orm:schema-tool:create
+    $ php bin/doctrine orm:schema-tool:drop --force
+    $ php bin/doctrine orm:schema-tool:create
 
 Or you can use the update functionality:
 
 ::
 
-    $ vendor/bin/doctrine orm:schema-tool:update --force
+    $ php bin/doctrine orm:schema-tool:update --force
 
 The updating of databases uses a diff algorithm for a given
 database schema. This is a cornerstone of the ``Doctrine\DBAL`` package,
@@ -571,7 +584,7 @@ let's update the database schema:
 
 ::
 
-    $ vendor/bin/doctrine orm:schema-tool:update --force --dump-sql
+    $ php bin/doctrine orm:schema-tool:update --force --dump-sql
 
 Specifying both flags ``--force`` and ``--dump-sql`` will cause the DDL
 statements to be executed and then printed to the screen.
@@ -1268,7 +1281,7 @@ class that holds the owning sides.
 Update your database schema by running:
 ::
 
-    $ vendor/bin/doctrine orm:schema-tool:update --force
+    $ php bin/doctrine orm:schema-tool:update --force
 
 
 Implementing more Requirements
diff --git a/lib/Doctrine/ORM/Tools/Console/ConsoleRunner.php b/lib/Doctrine/ORM/Tools/Console/ConsoleRunner.php
index 1bd4ab1ad54..90689fe04fd 100644
--- a/lib/Doctrine/ORM/Tools/Console/ConsoleRunner.php
+++ b/lib/Doctrine/ORM/Tools/Console/ConsoleRunner.php
@@ -122,6 +122,9 @@ public static function addCommands(Application $cli, ?EntityManagerProvider $ent
         );
     }
 
+    /**
+     * @deprecated This method will be removed in ORM 3.0 without replacement.
+     */
     public static function printCliConfigTemplate(): void
     {
         echo <<<'HELP'