diff --git a/src/Bridge/MoodlePlugin.php b/src/Bridge/MoodlePlugin.php
index 61678786..9f6efa09 100644
--- a/src/Bridge/MoodlePlugin.php
+++ b/src/Bridge/MoodlePlugin.php
@@ -256,6 +256,60 @@ public function getIgnores(): array
         return array_key_exists('filter', $config) ? $config['filter'] : [];
     }
 
+    /**
+     * Get ignore file information from subdirectory config files.
+     *
+     * Discovers .moodle-plugin-ci.yml files in all subdirectories of the plugin
+     * and merges their filter rules. notPaths entries are prefixed with the
+     * relative subdirectory path so they apply correctly when Finder is rooted
+     * at the main plugin directory.
+     *
+     * @return array{notPaths?: string[], notNames?: string[]}
+     */
+    private function getSubdirectoryIgnores(): array
+    {
+        $merged = [];
+
+        $configFiles = Finder::create()
+            ->files()
+            ->ignoreDotFiles(false)
+            ->in($this->directory)
+            ->name('.moodle-plugin-ci.yml')
+            ->depth('> 0')
+            ->ignoreUnreadableDirs();
+
+        foreach ($configFiles as $file) {
+            $config = Yaml::parse(file_get_contents($file->getRealPath()));
+
+            // Determine filter section: context-specific or generic (same logic as getIgnores).
+            $ignores = [];
+            if (!empty($this->context) && array_key_exists('filter-' . $this->context, $config)) {
+                $ignores = $config['filter-' . $this->context];
+            } elseif (array_key_exists('filter', $config)) {
+                $ignores = $config['filter'];
+            }
+
+            // Relative directory from the plugin root to this config file's directory.
+            $relativeDir = $file->getRelativePath();
+
+            // Prefix notPaths with the relative subdirectory path.
+            if (!empty($ignores['notPaths'])) {
+                foreach ($ignores['notPaths'] as $notPath) {
+                    $merged['notPaths'][] = $relativeDir . '/' . $notPath;
+                }
+            }
+
+            // notNames are filename patterns, applied globally.
+            if (!empty($ignores['notNames'])) {
+                foreach ($ignores['notNames'] as $notName) {
+                    $merged['notNames'][] = $notName;
+                }
+            }
+        }
+
+        return $merged;
+    }
+
     /**
      * Get a list of plugin files.
      *
@@ -286,6 +340,20 @@ public function getFiles(Finder $finder): array
             }
         }
 
+        // Merge ignores from subdirectory config files (e.g., subplugins).
+        $subIgnores = $this->getSubdirectoryIgnores();
+
+        if (!empty($subIgnores['notPaths'])) {
+            foreach ($subIgnores['notPaths'] as $notPath) {
+                $finder->notPath($notPath);
+            }
+        }
+        if (!empty($subIgnores['notNames'])) {
+            foreach ($subIgnores['notNames'] as $notName) {
+                $finder->notName($notName);
+            }
+        }
+
         $files = [];
         foreach ($finder as $file) {
             /* @var \SplFileInfo $file */
diff --git a/tests/Bridge/MoodlePluginTest.php b/tests/Bridge/MoodlePluginTest.php
index 1df95de7..c3a6e2ef 100644
--- a/tests/Bridge/MoodlePluginTest.php
+++ b/tests/Bridge/MoodlePluginTest.php
@@ -140,6 +140,96 @@ public function testGetFiles()
         $this->assertSame($expected, $files);
     }
 
+    public function testGetFilesWithSubdirectoryNotPaths()
+    {
+        // Create a subplugin directory with its own config.
+        $subDir = $this->pluginDir . '/subtype/mysub';
+        $this->fs->mkdir($subDir . '/vendor');
+        $this->fs->dumpFile($subDir . '/lib.php', '<?php // Subplugin lib.');
+        $this->fs->dumpFile($subDir . '/vendor/dep.php', '<?php // Vendor file to exclude.');
+
+        // Subplugin config excludes 'vendor' path.
+        $subConfig = ['filter' => ['notPaths' => ['vendor']]];
+        $this->fs->dumpFile($subDir . '/.moodle-plugin-ci.yml', Yaml::dump($subConfig));
+
+        // Main plugin config excludes 'ignore' path and 'ignore_name.php' name.
+        $mainConfig = ['filter' => ['notNames' => ['ignore_name.php'], 'notPaths' => ['ignore']]];
+        $this->fs->dumpFile($this->pluginDir . '/.moodle-plugin-ci.yml', Yaml::dump($mainConfig));
+
+        $finder = new Finder();
+        $finder->name('*.php');
+
+        $plugin = new MoodlePlugin($this->pluginDir);
+        $files  = $plugin->getFiles($finder);
+
+        // The subplugin's lib.php should be present.
+        $this->assertContains(realpath($subDir . '/lib.php'), $files);
+
+        // The subplugin's vendor/dep.php should be excluded by the subplugin config.
+        $this->assertNotContains(realpath($subDir . '/vendor/dep.php'), $files);
+    }
+
+    public function testGetFilesWithSubdirectoryContextFilter()
+    {
+        $subDir = $this->pluginDir . '/subtype/mysub';
+        $this->fs->mkdir($subDir);
+        $this->fs->dumpFile($subDir . '/excluded.php', '<?php // Should be excluded.');
+        $this->fs->dumpFile($subDir . '/included.php', '<?php // Should be included.');
+
+        // Context-specific filter for 'phpcs' command.
+        $subConfig = [
+            'filter'       => ['notPaths' => ['nonexistent']],
+            'filter-phpcs' => ['notNames' => ['excluded.php']],
+        ];
+        $this->fs->dumpFile($subDir . '/.moodle-plugin-ci.yml', Yaml::dump($subConfig));
+
+        // Main plugin config excludes 'ignore' path and 'ignore_name.php' name.
+        $mainConfig = ['filter' => ['notNames' => ['ignore_name.php'], 'notPaths' => ['ignore']]];
+        $this->fs->dumpFile($this->pluginDir . '/.moodle-plugin-ci.yml', Yaml::dump($mainConfig));
+
+        $finder = new Finder();
+        $finder->name('*.php');
+
+        $plugin          = new MoodlePlugin($this->pluginDir);
+        $plugin->context = 'phpcs';
+        $files           = $plugin->getFiles($finder);
+
+        $this->assertNotContains(realpath($subDir . '/excluded.php'), $files);
+        $this->assertContains(realpath($subDir . '/included.php'), $files);
+    }
+
+    public function testGetFilesWithMultipleSubdirectoryConfigs()
+    {
+        $sub1Dir = $this->pluginDir . '/subtype1/sub1';
+        $sub2Dir = $this->pluginDir . '/subtype2/sub2';
+        $this->fs->mkdir($sub1Dir . '/generated');
+        $this->fs->mkdir($sub2Dir . '/tmp');
+        $this->fs->dumpFile($sub1Dir . '/lib.php', '<?php // Sub1 lib.');
+        $this->fs->dumpFile($sub1Dir . '/generated/out.php', '<?php // Generated.');
+        $this->fs->dumpFile($sub2Dir . '/lib.php', '<?php // Sub2 lib.');
+        $this->fs->dumpFile($sub2Dir . '/tmp/cache.php', '<?php // Cached.');
+
+        $this->fs->dumpFile($sub1Dir . '/.moodle-plugin-ci.yml',
+            Yaml::dump(['filter' => ['notPaths' => ['generated']]]));
+        $this->fs->dumpFile($sub2Dir . '/.moodle-plugin-ci.yml',
+            Yaml::dump(['filter' => ['notPaths' => ['tmp']]]));
+
+        // Main plugin config excludes 'ignore' path and 'ignore_name.php' name.
+        $mainConfig = ['filter' => ['notNames' => ['ignore_name.php'], 'notPaths' => ['ignore']]];
+        $this->fs->dumpFile($this->pluginDir . '/.moodle-plugin-ci.yml', Yaml::dump($mainConfig));
+
+        $finder = new Finder();
+        $finder->name('*.php');
+
+        $plugin = new MoodlePlugin($this->pluginDir);
+        $files  = $plugin->getFiles($finder);
+
+        $this->assertNotContains(realpath($sub1Dir . '/generated/out.php'), $files);
+        $this->assertNotContains(realpath($sub2Dir . '/tmp/cache.php'), $files);
+        $this->assertContains(realpath($sub1Dir . '/lib.php'), $files);
+        $this->assertContains(realpath($sub2Dir . '/lib.php'), $files);
+    }
+
     public function testGetRelativeFiles()
     {
         // Ignore some files for better testing.