diff --git a/src/Composer/Plugin/PluginManager.php b/src/Composer/Plugin/PluginManager.php
index c20d403fa..3f88f6994 100644
--- a/src/Composer/Plugin/PluginManager.php
+++ b/src/Composer/Plugin/PluginManager.php
@@ -216,6 +216,17 @@ class PluginManager
         $globalRepo = $this->globalComposer !== null ? $this->globalComposer->getRepositoryManager()->getLocalRepository() : null;
 
         $rootPackage = clone $this->composer->getPackage();
+
+        // clear files autoload rules from the root package as the root dependencies are not
+        // necessarily all present yet when booting this runtime autoloader
+        $rootPackageAutoloads = $rootPackage->getAutoload();
+        $rootPackageAutoloads['files'] = array();
+        $rootPackage->setAutoload($rootPackageAutoloads);
+        $rootPackageAutoloads = $rootPackage->getDevAutoload();
+        $rootPackageAutoloads['files'] = array();
+        $rootPackage->setDevAutoload($rootPackageAutoloads);
+        unset($rootPackageAutoloads);
+
         $rootPackageRepo = new RootPackageRepository($rootPackage);
         $installedRepo = new InstalledRepository(array($localRepo, $rootPackageRepo));
         if ($globalRepo) {
diff --git a/tests/Composer/Test/Plugin/Fixtures/files_autoload_which_should_not_run.php b/tests/Composer/Test/Plugin/Fixtures/files_autoload_which_should_not_run.php
new file mode 100644
index 000000000..392b5bffd
--- /dev/null
+++ b/tests/Composer/Test/Plugin/Fixtures/files_autoload_which_should_not_run.php
@@ -0,0 +1,3 @@
+<?php
+
+throw new \LogicException('This file should not be autoloaded');
diff --git a/tests/Composer/Test/Plugin/PluginInstallerTest.php b/tests/Composer/Test/Plugin/PluginInstallerTest.php
index 6466571d7..5091617a7 100644
--- a/tests/Composer/Test/Plugin/PluginInstallerTest.php
+++ b/tests/Composer/Test/Plugin/PluginInstallerTest.php
@@ -152,6 +152,28 @@ class PluginInstallerTest extends TestCase
         );
     }
 
+    public function testInstallPluginWithRootPackageHavingFilesAutoload()
+    {
+        $this->repository
+            ->expects($this->any())
+            ->method('getPackages')
+            ->will($this->returnValue(array()));
+        $installer = new PluginInstaller($this->io, $this->composer);
+        $this->pm->loadInstalledPlugins();
+
+        $this->autoloadGenerator->setDevMode(true);
+        $this->composer->getPackage()->setAutoload(array('files' => array(__DIR__ . '/Fixtures/files_autoload_which_should_not_run.php')));
+        $this->composer->getPackage()->setDevAutoload(array('files' => array(__DIR__ . '/Fixtures/files_autoload_which_should_not_run.php')));
+        $installer->install($this->repository, $this->packages[0]);
+
+        $plugins = $this->pm->getPlugins();
+        $this->assertEquals(
+            'activate v1'.PHP_EOL,
+            $this->io->getOutput()
+        );
+        $this->assertEquals('installer-v1', $plugins[0]->version);  // @phpstan-ignore-line
+    }
+
     public function testInstallMultiplePlugins()
     {
         $this->repository