diff --git a/bin/moodle-plugin-ci b/bin/moodle-plugin-ci
index 4972d49c..386d4787 100755
--- a/bin/moodle-plugin-ci
+++ b/bin/moodle-plugin-ci
@@ -48,7 +48,16 @@ if (file_exists(__DIR__ . '/../../../autoload.php')) {
 define('MOODLE_PLUGIN_CI_VERSION', '4.1.3');
 
 define('MOODLE_PLUGIN_CI_BOXED', '@is_boxed@');
-define('ENV_FILE', dirname(__DIR__) . '/.env');
+
+// If we are running moodle-plugin-ci within a PHAR, we need to set the
+// path to the dotenv file differently.
+if (\Phar::running() !== '') {
+    // The .env file is in the same directory than the phar.
+    define('ENV_FILE', dirname(\Phar::running(false)) . '/.env');
+} else {
+    // The .env file is in the root directory of the moodle-plugin-ci project.
+    define('ENV_FILE', dirname(__DIR__) . '/.env');
+}
 
 if (file_exists(ENV_FILE)) {
     // Use this file because PHP cannot write to the environment.
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index 566ed1b0..ddd7b8be 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -10,6 +10,7 @@ The format of this change log follows the advice given at [Keep a CHANGELOG](htt
 
 ## [Unreleased]
 ### Fixed
+- Fix the `.env` support when running from within the PHAR archive.
 - Fix the `mustache` command to work from within the PHAR archive.
 - Fix the `phpcs` and `phpcbf` commands to work from within the PHAR archive.
 
diff --git a/src/Command/AbstractPluginCommand.php b/src/Command/AbstractPluginCommand.php
index a166d2d9..4dee6ac0 100644
--- a/src/Command/AbstractPluginCommand.php
+++ b/src/Command/AbstractPluginCommand.php
@@ -38,7 +38,7 @@ protected function configure(): void
 
     protected function initialize(InputInterface $input, OutputInterface $output): void
     {
-        if (!isset($this->plugin)) {
+        if (!isset($this->plugin) && $input->getArgument('plugin') !== null) {
             $validate     = new Validate();
             $pluginDir    = realpath($validate->directory($input->getArgument('plugin')));
             $this->plugin = new MoodlePlugin($pluginDir);