diff --git a/src/Context/FeatureContext.php b/src/Context/FeatureContext.php
index 2eb061db7..2e3fe67b1 100644
--- a/src/Context/FeatureContext.php
+++ b/src/Context/FeatureContext.php
@@ -38,6 +38,11 @@ class FeatureContext implements SnippetAcceptingContext {
 	 */
 	private static $run_dir;
 
+	/**
+	 * The Directory that 'composer behat' is run from, assumed to always be the top level project folder
+	 */
+	private static $behat_run_dir;
+
 	/**
 	 * Where WordPress core is downloaded to for caching, and which is copied to RUN_DIR during a "Given a WP installation" step. Lives until manually deleted.
 	 */
@@ -286,9 +291,10 @@ private static function get_process_env_variables() {
 
 		$path_separator = Utils\is_windows() ? ';' : ':';
 		$env            = [
-			'PATH'      => $bin_path . $path_separator . getenv( 'PATH' ),
-			'BEHAT_RUN' => 1,
-			'HOME'      => sys_get_temp_dir() . '/wp-cli-home',
+			'PATH'         => $bin_path . $path_separator . getenv( 'PATH' ),
+			'BEHAT_RUN'    => 1,
+			'HOME'         => sys_get_temp_dir() . '/wp-cli-home',
+			'TEST_RUN_DIR' => self::$behat_run_dir,
 		];
 
 		$config_path = getenv( 'WP_CLI_CONFIG_PATH' );
@@ -371,6 +377,7 @@ private static function get_behat_internal_variables() {
 			'FRAMEWORK_ROOT' => realpath( $framework_root ),
 			'SRC_DIR'        => realpath( dirname( dirname( __DIR__ ) ) ),
 			'PROJECT_DIR'    => realpath( dirname( dirname( dirname( dirname( dirname( __DIR__ ) ) ) ) ) ),
+			'TEST_RUN_DIR'   => self::$behat_run_dir,
 		];
 
 		return $variables;
@@ -475,6 +482,7 @@ public static function prepare( BeforeSuiteScope $scope ) {
 		if ( false !== self::$log_run_times ) {
 			self::log_run_times_before_suite( $scope );
 		}
+		self::$behat_run_dir = getcwd();
 
 		$result = Process::create( 'wp cli info', null, self::get_process_env_variables() )->run_check();
 		echo "{$result->stdout}\n";
@@ -521,7 +529,6 @@ public function beforeScenario( BeforeScenarioScope $scope ) {
 		if ( self::$log_run_times ) {
 			self::log_run_times_before_scenario( $scope );
 		}
-
 		$this->variables = array_merge(
 			$this->variables,
 			self::get_behat_internal_variables()
@@ -693,8 +700,31 @@ public function __construct() {
 	 */
 	public function get_command_with_coverage( $cmd ) {
 		$with_code_coverage = (string) getenv( 'WP_CLI_TEST_COVERAGE' );
+
 		if ( \in_array( $with_code_coverage, [ 'true', '1' ], true ) ) {
-			return preg_replace( '/(^wp )|( wp )|(\/wp )/', '$1$2$3--require={SRC_DIR}/utils/generate-coverage.php ', $cmd );
+
+			$modify_command = function ( $part ) {
+				if ( preg_match( '/(^wp )|( wp )|(\/wp )/', $part ) ) {
+					$part = preg_replace( '/(^wp )|( wp )|(\/wp )/', '$1$2$3', $part );
+
+					$require_path = '{TEST_RUN_DIR}/vendor/wp-cli/wp-cli-tests/utils/generate-coverage.php';
+					if ( ! file_exists( $this->variables['TEST_RUN_DIR'] . '/vendor/wp-cli/wp-cli-tests/utils/generate-coverage.php' ) ) {
+						// This file is not vendored inside the wp-cli-tests project
+						$require_path = '{TEST_RUN_DIR}/utils/generate-coverage.php';
+					}
+					$part .= " --require={$require_path}";
+
+				}
+				return $part;
+			};
+
+			if ( strpos( $cmd, '|' ) !== false ) {
+				$parts = explode( '|', $cmd );
+				$parts = array_map( $modify_command, $parts );
+				$cmd   = implode( '|', $parts );
+			} else {
+				$cmd = $modify_command( $cmd );
+			}
 		}
 
 		return $cmd;
diff --git a/utils/generate-coverage.php b/utils/generate-coverage.php
index 6a19e806e..d324fe757 100644
--- a/utils/generate-coverage.php
+++ b/utils/generate-coverage.php
@@ -11,15 +11,54 @@
 use SebastianBergmann\CodeCoverage\Filter;
 use SebastianBergmann\CodeCoverage\Report\Clover;
 
-$root_folder = realpath( dirname( __DIR__ ) );
+
+$project_dir = (string) getenv( 'TEST_RUN_DIR' );
 
 if ( ! class_exists( 'SebastianBergmann\CodeCoverage\Filter' ) ) {
-	require "{$root_folder}/vendor/autoload.php";
+	if ( ! file_exists( $project_dir . '/vendor/autoload.php' ) ) {
+		die( 'Could not load dependencies for generating code coverage' );
+	}
+	require "{$project_dir}/vendor/autoload.php";
+}
+
+$filtered_items = new CallbackFilterIterator(
+	new DirectoryIterator( $project_dir ),
+	function ( $file ) {
+		// Allow directories named "php" or "src"
+		if ( $file->isDir() && in_array( $file->getFilename(), [ 'php', 'src' ], true ) ) {
+			return true;
+		}
+
+		// Allow top-level files ending in "-command.php"
+		if ( $file->isFile() && false !== strpos( $file->getFilename(), '-command.php' ) ) {
+			return true;
+		}
+
+		return false;
+	}
+);
+
+$files = [];
+
+foreach ( $filtered_items as $item ) {
+	if ( $item->isDir() ) {
+		foreach (
+			new RecursiveIteratorIterator(
+				new RecursiveDirectoryIterator( $item->getPathname(), RecursiveDirectoryIterator::SKIP_DOTS )
+			) as $file
+		) {
+			if ( $file->isFile() && $file->getExtension() === 'php' ) {
+				$files[] = $file->getPathname();
+			}
+		}
+	} else {
+		$files[] = $item->getPathname();
+	}
 }
 
 $filter = new Filter();
-$filter->includeDirectory( "{$root_folder}/includes" );
-$filter->includeFiles( array( "{$root_folder}/plugin.php" ) );
+
+$filter->includeFiles( $files );
 
 $coverage = new CodeCoverage(
 	( new Selector() )->forLineCoverage( $filter ),
@@ -37,11 +76,9 @@
 $coverage->start( $name );
 
 register_shutdown_function(
-	static function () use ( $coverage, $feature, $scenario, $name ) {
+	static function () use ( $coverage, $feature, $scenario, $name, $project_dir ) {
 		$coverage->stop();
 
-		$project_dir = (string) getenv( 'BEHAT_PROJECT_DIR' );
-
 		$feature_suffix  = preg_replace( '/[^a-z0-9]+/', '-', strtolower( $feature ) );
 		$scenario_suffix = preg_replace( '/[^a-z0-9]+/', '-', strtolower( $scenario ) );
 		$db_type         = strtolower( getenv( 'WP_CLI_TEST_DBTYPE' ) );