diff --git a/includes/CLI/Plugin_Check_Command.php b/includes/CLI/Plugin_Check_Command.php
index 05f93faad..255af27c3 100644
--- a/includes/CLI/Plugin_Check_Command.php
+++ b/includes/CLI/Plugin_Check_Command.php
@@ -13,8 +13,6 @@
 use WordPress\Plugin_Check\Checker\Check_Repository;
 use WordPress\Plugin_Check\Checker\CLI_Runner;
 use WordPress\Plugin_Check\Checker\Default_Check_Repository;
-use WordPress\Plugin_Check\Checker\Runtime_Check;
-use WordPress\Plugin_Check\Checker\Runtime_Environment_Setup;
 use WordPress\Plugin_Check\Plugin_Context;
 use WordPress\Plugin_Check\Utilities\Plugin_Request_Utility;
 use WP_CLI;
@@ -192,25 +190,16 @@ static function ( $dirs ) use ( $excluded_files ) {
 			);
 		}
 
-		$checks_to_run = array();
 		try {
 			$runner->set_experimental_flag( $options['include-experimental'] );
 			$runner->set_check_slugs( $checks );
 			$runner->set_plugin( $plugin );
 			$runner->set_categories( $categories );
 			$runner->set_slug( $options['slug'] );
-
-			$checks_to_run = $runner->get_checks_to_run();
 		} catch ( Exception $error ) {
 			WP_CLI::error( $error->getMessage() );
 		}
 
-		if ( $this->has_runtime_check( $checks_to_run ) ) {
-			WP_CLI::line( __( 'Setting up runtime environment.', 'plugin-check' ) );
-			$runtime_setup = new Runtime_Environment_Setup();
-			$runtime_setup->set_up();
-		}
-
 		$result = false;
 		// Run checks against the plugin.
 		try {
@@ -218,21 +207,11 @@ static function ( $dirs ) use ( $excluded_files ) {
 		} catch ( Exception $error ) {
 			Plugin_Request_Utility::destroy_runner();
 
-			if ( isset( $runtime_setup ) ) {
-				$runtime_setup->clean_up();
-				WP_CLI::line( __( 'Cleaning up runtime environment.', 'plugin-check' ) );
-			}
-
 			WP_CLI::error( $error->getMessage() );
 		}
 
 		Plugin_Request_Utility::destroy_runner();
 
-		if ( isset( $runtime_setup ) ) {
-			$runtime_setup->clean_up();
-			WP_CLI::line( __( 'Cleaning up runtime environment.', 'plugin-check' ) );
-		}
-
 		// Get errors and warnings from the results.
 		$errors = array();
 		if ( $result && empty( $assoc_args['ignore-errors'] ) ) {
@@ -642,24 +621,6 @@ private function display_results( $formatter, $file_name, $file_results ) {
 		WP_CLI::line();
 	}
 
-	/**
-	 * Checks for a Runtime_Check in a list of checks.
-	 *
-	 * @since 1.0.0
-	 *
-	 * @param array $checks An array of Check instances.
-	 * @return bool True if a Runtime_Check exists in the array, false if not.
-	 */
-	private function has_runtime_check( array $checks ) {
-		foreach ( $checks as $check ) {
-			if ( $check instanceof Runtime_Check ) {
-				return true;
-			}
-		}
-
-		return false;
-	}
-
 	/**
 	 * Returns check results filtered by severity level.
 	 *
diff --git a/includes/Checker/Abstract_Check_Runner.php b/includes/Checker/Abstract_Check_Runner.php
index 368418da3..001f1b3f5 100644
--- a/includes/Checker/Abstract_Check_Runner.php
+++ b/includes/Checker/Abstract_Check_Runner.php
@@ -310,8 +310,6 @@ final public function set_categories( $categories ) {
 	 * @throws Exception Thrown exception when preparation fails.
 	 */
 	final public function prepare() {
-		$cleanup_functions = array();
-
 		if ( $this->initialized_early ) {
 			/*
 			 * When initialized early, plugins are not loaded yet when this method is called.
@@ -334,9 +332,9 @@ final public function prepare() {
 			$initialize_runtime = $this->has_runtime_check( $this->get_checks_to_run() );
 		}
 
+		$cleanup_functions = array();
 		if ( $initialize_runtime ) {
-			$preparation         = new Universal_Runtime_Preparation( $this->get_check_context() );
-			$cleanup_functions[] = $preparation->prepare();
+			$cleanup_functions = $this->initialize_runtime();
 		}
 
 		if ( $this->delete_plugin_folder ) {
@@ -489,6 +487,18 @@ final public function get_checks_to_run() {
 		return $collection->to_map();
 	}
 
+	/**
+	 * Initializes the runtime environment so that runtime checks can be run against a separate set of database tables.
+	 *
+	 * @since 1.3.0
+	 *
+	 * @return callable[] Array of cleanup functions to run after the process has completed.
+	 */
+	protected function initialize_runtime(): array {
+		$preparation = new Universal_Runtime_Preparation( $this->get_check_context() );
+		return array( $preparation->prepare() );
+	}
+
 	/**
 	 * Checks whether the current environment allows for runtime checks to be used.
 	 *
diff --git a/includes/Checker/CLI_Runner.php b/includes/Checker/CLI_Runner.php
index 53ba12224..7b92dcf9f 100644
--- a/includes/Checker/CLI_Runner.php
+++ b/includes/Checker/CLI_Runner.php
@@ -178,6 +178,31 @@ protected function get_slug_param() {
 		return $slug;
 	}
 
+	/**
+	 * Initializes the runtime environment so that runtime checks can be run against a separate set of database tables.
+	 *
+	 * @since 1.3.0
+	 *
+	 * @return callable[] Array of cleanup functions to run after the process has completed.
+	 */
+	protected function initialize_runtime(): array {
+		/*
+		 * Since for WP-CLI all checks are run in a single process, we should set up the runtime environment (i.e.
+		 * install the separate database tables) as part of this step.
+		 * This way it runs before the regular runtime preparations, just like it does for the AJAX based flow, where
+		 * they are invoked in a separate request prior to the requests performing actual checks.
+		 */
+		$runtime_setup = new Runtime_Environment_Setup();
+		$runtime_setup->set_up();
+
+		$cleanup_functions   = parent::initialize_runtime();
+		$cleanup_functions[] = function () use ( $runtime_setup ) {
+			$runtime_setup->clean_up();
+		};
+
+		return $cleanup_functions;
+	}
+
 	/**
 	 * Checks whether the current environment allows for runtime checks to be used.
 	 *
diff --git a/includes/Checker/Runtime_Environment_Setup.php b/includes/Checker/Runtime_Environment_Setup.php
index bd84b784c..40c14dd95 100644
--- a/includes/Checker/Runtime_Environment_Setup.php
+++ b/includes/Checker/Runtime_Environment_Setup.php
@@ -28,9 +28,15 @@ public function set_up() {
 
 		require_once ABSPATH . '/wp-admin/includes/upgrade.php';
 
+		// Get the existing site URL.
+		$site_url = get_option( 'siteurl' );
+
 		// Get the existing active plugins.
 		$active_plugins = get_option( 'active_plugins' );
 
+		// Get the existing active theme.
+		$active_theme = get_option( 'stylesheet' );
+
 		// Get the existing permalink structure.
 		$permalink_structure = get_option( 'permalink_structure' );
 
@@ -48,29 +54,25 @@ public function set_up() {
 			add_action(
 				'populate_options',
 				static function () use ( $permalink_structure ) {
+					/*
+					 * If pretty permalinks are not used, temporarily enable them by setting a permalink structure, to
+					 * avoid flushing rewrite rules in wp_install_maybe_enable_pretty_permalinks().
+					 * Afterwards, on the 'wp_install' action, set the original (empty) permalink structure.
+					 */
+					if ( ! $permalink_structure ) {
+						add_action(
+							'wp_install',
+							static function () use ( $permalink_structure ) {
+								update_option( 'permalink_structure', $permalink_structure );
+							}
+						);
+						$permalink_structure = '/%postname%/';
+					}
 					add_option( 'permalink_structure', $permalink_structure );
 				}
 			);
 
-			if ( ! isset( $_SERVER['HTTP_HOST'] ) ) {
-				$site_url             = get_option( 'siteurl' );
-				$_SERVER['HTTP_HOST'] = preg_replace( '#^https?://#', '', rtrim( $site_url, '/' ) );
-			}
-
-			// Do not send post-install notification email, see https://github.com/WordPress/plugin-check/issues/424.
-			add_filter( 'pre_wp_mail', '__return_false' );
-
-			wp_install(
-				'Plugin Check',
-				'plugincheck',
-				'demo@plugincheck.test',
-				false
-			);
-
-			remove_filter( 'pre_wp_mail', '__return_false' );
-
-			// Activate the same plugins in the test environment.
-			update_option( 'active_plugins', $active_plugins );
+			$this->install_wordpress( $site_url, $active_theme, $active_plugins );
 		}
 
 		// Restore the old prefix.
@@ -186,4 +188,57 @@ public function can_set_up() {
 
 		return false;
 	}
+
+	/**
+	 * Installs WordPress, while providing tweaks to allow for early execution of the install process.
+	 *
+	 * @since 1.3.0
+	 *
+	 * @param string   $active_siteurl The actual site's site URL.
+	 * @param string   $active_theme   The actual site's theme slug.
+	 * @param string[] $active_plugins The actual site's list of plugin basenames.
+	 */
+	private function install_wordpress( string $active_siteurl, string $active_theme, array $active_plugins ): void {
+		if ( ! isset( $_SERVER['HTTP_HOST'] ) ) {
+			$site_url             = $active_siteurl;
+			$_SERVER['HTTP_HOST'] = preg_replace( '#^https?://#', '', rtrim( $site_url, '/' ) );
+		}
+
+		// Do not send post-install notification email, see https://github.com/WordPress/plugin-check/issues/424.
+		add_filter( 'pre_wp_mail', '__return_false' );
+
+		// The `wp_install()` function requires the WP_DEFAULT_THEME constant to be set.
+		if ( ! defined( 'WP_DEFAULT_THEME' ) ) {
+			define( 'WP_DEFAULT_THEME', $active_theme );
+		}
+
+		// The `wp_install()` function requires some pluggable functions like `get_user_by()` to be loaded.
+		if ( ! function_exists( 'get_user_by' ) ) {
+			require_once ABSPATH . '/wp-includes/pluggable.php';
+		}
+
+		/*
+		 * Cookie constants need to be set before installation, which normally happens immediately after
+		 * 'muplugins_loaded', which is when the logic here typically runs. It is therefore safe to call these
+		 * functions here already.
+		 */
+		if ( doing_action( 'muplugins_loaded' ) || ! did_action( 'muplugins_loaded' ) ) {
+			if ( is_multisite() ) {
+				ms_cookie_constants();
+			}
+			wp_cookie_constants();
+		}
+
+		wp_install(
+			'Plugin Check',
+			'plugincheck',
+			'demo@plugincheck.test',
+			false
+		);
+
+		remove_filter( 'pre_wp_mail', '__return_false' );
+
+		// Activate the same plugins in the test environment.
+		update_option( 'active_plugins', $active_plugins );
+	}
 }
diff --git a/tests/behat/features/plugin-check.feature b/tests/behat/features/plugin-check.feature
index f7bca75a5..287c14a51 100644
--- a/tests/behat/features/plugin-check.feature
+++ b/tests/behat/features/plugin-check.feature
@@ -548,14 +548,6 @@ Feature: Test that the WP-CLI command works.
     # Running runtime checks, including the one from pcp-addon
     When I run the WP-CLI command `plugin check foo-sample --fields=code,type --format=csv --require=./wp-content/plugins/plugin-check/cli.php`
     Then STDOUT should contain:
-      """
-      Setting up runtime environment.
-      """
-    And STDOUT should contain:
-      """
-      Cleaning up runtime environment.
-      """
-    And STDOUT should contain:
       """
       WordPress.WP.EnqueuedResourceParameters.NotInFooter,WARNING
       """
@@ -568,14 +560,6 @@ Feature: Test that the WP-CLI command works.
     # Same again, to verify object-cache.php was properly cleared again
     When I run the WP-CLI command `plugin check foo-sample --fields=code,type --format=csv --require=./wp-content/plugins/plugin-check/cli.php`
     Then STDOUT should contain:
-      """
-      Setting up runtime environment.
-      """
-    And STDOUT should contain:
-      """
-      Cleaning up runtime environment.
-      """
-    And STDOUT should contain:
       """
       WordPress.WP.EnqueuedResourceParameters.NotInFooter,WARNING
       """