diff --git a/includes/Checker/Checks/Abstract_PHP_CodeSniffer_Check.php b/includes/Checker/Checks/Abstract_PHP_CodeSniffer_Check.php
index d3bde6a40..910c139fd 100644
--- a/includes/Checker/Checks/Abstract_PHP_CodeSniffer_Check.php
+++ b/includes/Checker/Checks/Abstract_PHP_CodeSniffer_Check.php
@@ -110,21 +110,24 @@ final public function run( Check_Result $result ) {
 		$_SERVER['argv'] = $this->parse_argv( $args, $defaults );
 
 		// Run PHPCS.
+		$php_codesniffer_error_handler = $this->register_php_codesniffer_error_handler();
 		try {
 			ob_start();
-			$runner = new Runner();
-			$runner->runPHPCS();
+			$this->run_php_codesniffer();
 			$reports = ob_get_clean();
 		} catch ( Exception $e ) {
-			$_SERVER['argv'] = $orig_cmd_args;
+			if ( ob_get_level() > 0 ) {
+				ob_end_clean();
+			}
 			throw $e;
-		}
+		} finally {
+			$this->restore_php_codesniffer_error_handler( $php_codesniffer_error_handler );
+			// Reset installed_paths.
+			Config::setConfigData( 'installed_paths', $installed_paths, true );
 
-		// Reset installed_paths.
-		Config::setConfigData( 'installed_paths', $installed_paths, true );
-
-		// Restore original arguments.
-		$_SERVER['argv'] = $orig_cmd_args;
+			// Restore original arguments.
+			$_SERVER['argv'] = $orig_cmd_args;
+		}
 
 		// Parse the reports into data to add to the overall $result.
 		$reports = json_decode( trim( $reports ), true );
@@ -154,6 +157,22 @@ final public function run( Check_Result $result ) {
 		}
 	}
 
+	/**
+	 * Runs PHP_CodeSniffer.
+	 *
+	 * @since n.e.x.t
+	 */
+	protected function run_php_codesniffer() {
+		/*
+		 * PHPStan cannot infer the class_exists() check performed by run().
+		 *
+		 * @phpstan-ignore-next-line
+		 */
+		$runner = new Runner();
+		/* @phpstan-ignore-next-line */
+		$runner->runPHPCS();
+	}
+
 	/**
 	 * Parse the command arguments.
 	 *
@@ -229,6 +248,64 @@ private function get_argv_defaults( Check_Result $result ): array {
 		return $defaults;
 	}
 
+	/**
+	 * Registers an error handler for known PHPCS notices.
+	 *
+	 * @since n.e.x.t
+	 */
+	private function register_php_codesniffer_error_handler() {
+		$previous_error_handler = null;
+
+		$error_handler = static function ( $errno, $errstr, $errfile, $errline ) use ( &$previous_error_handler ) {
+			$normalized_file = wp_normalize_path( $errfile );
+
+			if (
+				E_DEPRECATED === $errno &&
+				false !== strpos( $errstr, 'auto_detect_line_endings is deprecated' ) &&
+				false !== strpos( $normalized_file, 'vendor/squizlabs/php_codesniffer/src/Runner.php' )
+			) {
+				return true;
+			}
+
+			/*
+			 * PHPStan cannot infer the deferred assignment after the closure is created.
+			 *
+			 * @phpstan-ignore-next-line
+			 */
+			if ( is_callable( $previous_error_handler ) ) {
+				return (bool) call_user_func( $previous_error_handler, $errno, $errstr, $errfile, $errline );
+			}
+
+			return false;
+		};
+
+		$previous_error_handler = set_error_handler( $error_handler );
+
+		return $error_handler;
+	}
+
+	/**
+	 * Restores the error handler that was active before running PHP_CodeSniffer.
+	 *
+	 * PHP_CodeSniffer registers its own error handler while processing files. If
+	 * processing throws, PHP_CodeSniffer does not restore that handler, so it must
+	 * be removed before the temporary deprecation handler can be restored.
+	 *
+	 * @since n.e.x.t
+	 *
+	 * @param callable $php_codesniffer_error_handler The temporary error handler registered before running PHP_CodeSniffer.
+	 */
+	private function restore_php_codesniffer_error_handler( $php_codesniffer_error_handler ) {
+
+		$current_error_handler = set_error_handler( $php_codesniffer_error_handler );
+		restore_error_handler();
+
+		if ( $current_error_handler !== $php_codesniffer_error_handler ) {
+			restore_error_handler();
+		}
+
+		restore_error_handler();
+	}
 	/**
 	 * Resets \PHP_CodeSniffer\Config::$overriddenDefaults to prevent
 	 * incorrect results when running multiple checks.
diff --git a/tests/phpunit/tests/Checker/Checks/Plugin_Review_PHPCS_Check_Tests.php b/tests/phpunit/tests/Checker/Checks/Plugin_Review_PHPCS_Check_Tests.php
index 0e0779dba..e23c36672 100644
--- a/tests/phpunit/tests/Checker/Checks/Plugin_Review_PHPCS_Check_Tests.php
+++ b/tests/phpunit/tests/Checker/Checks/Plugin_Review_PHPCS_Check_Tests.php
@@ -161,4 +161,76 @@ public function test_run_without_errors() {
 		$this->assertEquals( 0, $check_result->get_error_count() );
 		$this->assertEquals( 0, $check_result->get_warning_count() );
 	}
+
+	public function test_run_suppresses_phpcs_auto_detect_line_endings_deprecation() {
+
+		$plugin_review_phpcs_check = new Plugin_Review_PHPCS_Check();
+		$check_context             = new Check_Context( UNIT_TESTS_PLUGIN_DIR . 'test-plugin-review-phpcs-without-errors/load.php' );
+		$check_result              = new Check_Result( $check_context );
+
+		$previous_error_handler = null;
+
+		$previous_error_handler = set_error_handler(
+			static function ( $errno, $errstr, $errfile, $errline ) use ( &$previous_error_handler ) {
+				if ( E_DEPRECATED === $errno && false !== strpos( $errstr, 'auto_detect_line_endings is deprecated' ) ) {
+					throw new ErrorException( $errstr, 0, $errno, $errfile, $errline );
+				}
+
+				if ( is_callable( $previous_error_handler ) ) {
+					return (bool) call_user_func( $previous_error_handler, $errno, $errstr, $errfile, $errline );
+				}
+
+				return false;
+			}
+		);
+
+		try {
+			$plugin_review_phpcs_check->run( $check_result );
+		} finally {
+			restore_error_handler();
+		}
+
+		$this->assertEquals( 0, $check_result->get_error_count() );
+		$this->assertEquals( 0, $check_result->get_warning_count() );
+	}
+
+	public function test_run_restores_original_error_handler_when_phpcs_throws() {
+		$plugin_review_phpcs_check = new class() extends Plugin_Review_PHPCS_Check {
+			protected function run_php_codesniffer() {
+				set_error_handler(
+					static function () {
+						return false;
+					}
+				);
+				throw new Exception( 'Test exception after PHP_CodeSniffer registers its error handler.' );
+			}
+		};
+		$check_context             = new Check_Context( UNIT_TESTS_PLUGIN_DIR . 'test-plugin-review-phpcs-without-errors/load.php' );
+		$check_result              = new Check_Result( $check_context );
+		$original_error_handler    = static function () {
+			return false;
+		};
+
+		set_error_handler( $original_error_handler );
+
+		try {
+			try {
+				$plugin_review_phpcs_check->run( $check_result );
+				$this->fail( 'Expected PHP_CodeSniffer to throw an exception.' );
+			} catch ( Exception $e ) {
+				$this->assertSame( 'Test exception after PHP_CodeSniffer registers its error handler.', $e->getMessage() );
+			}
+
+			$current_error_handler = set_error_handler(
+				static function () {
+					return false;
+				}
+			);
+			restore_error_handler();
+
+			$this->assertSame( $original_error_handler, $current_error_handler );
+		} finally {
+			restore_error_handler();
+		}
+	}
 }