diff --git a/CHANGELOG-v3.md b/CHANGELOG-v3.md
index 80de64e15ec..3ccce7b4aac 100644
--- a/CHANGELOG-v3.md
+++ b/CHANGELOG-v3.md
@@ -7,6 +7,7 @@
 
 ### Changed
 - The `app/migrate` web action now applies pending `project.yaml` changes, if the `useProjectConfigFile` config setting is enabled.
+- Project Config map now uses relative file paths with aliases instead of absolute paths. ([#3546](https://github.com/craftcms/cms/issues/3546))
 
 ### Fixed
 - Fixed a bug where restoring elements belonging to deleted sites via `project.yaml` would throw an error.
diff --git a/src/migrations/m181213_102500_remove_absolue_paths_from_configmap.php b/src/migrations/m181213_102500_remove_absolue_paths_from_configmap.php
new file mode 100644
index 00000000000..bec3533922e
--- /dev/null
+++ b/src/migrations/m181213_102500_remove_absolue_paths_from_configmap.php
@@ -0,0 +1,44 @@
+<?php
+
+namespace craft\migrations;
+
+use Craft;
+use craft\db\Migration;
+use craft\db\Query;
+use craft\helpers\ArrayHelper;
+use craft\services\Sections;
+use yii\helpers\Json;
+
+/**
+ * m181213_102500_remove_absolue_paths_from_configmap migration.
+ */
+class m181213_102500_remove_absolue_paths_from_configmap extends Migration
+{
+    /**
+     * @inheritdoc
+     */
+    public function safeUp()
+    {
+        $info = Craft::$app->getInfo();
+        $configMap = Json::decode($info->configMap) ?? [];
+
+        foreach ($configMap as &$filePath) {
+            $filePath = Craft::alias($filePath);
+        }
+
+        $info->configMap = $configMap;
+
+        Craft::$app->saveInfo($info);
+
+        return true;
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function safeDown()
+    {
+        echo "m181213_102500_remove_absolue_paths_from_configmap cannot be reverted.\n";
+        return false;
+    }
+}
diff --git a/src/services/ProjectConfig.php b/src/services/ProjectConfig.php
index 0d2db07fe15..3c214361e95 100644
--- a/src/services/ProjectConfig.php
+++ b/src/services/ProjectConfig.php
@@ -572,7 +572,13 @@ public function saveModifiedConfigData()
             $info = Craft::$app->getInfo();
 
             if ($this->_updateConfigMap && $this->_useConfigFile()) {
-                $info->configMap = Json::encode($this->_generateConfigMap());
+                $configMap = $this->_generateConfigMap();
+
+                foreach ($configMap as &$filePath) {
+                    $filePath = Craft::alias($filePath);
+                }
+
+                $info->configMap = Json::encode($configMap);
             }
 
             if ($this->_updateConfig) {
@@ -865,7 +871,13 @@ private function _getStoredConfigMap(): array
             return $this->_configMap;
         }
 
-        return $this->_configMap = Json::decode(Craft::$app->getInfo()->configMap) ?? [];
+        $configMap = Json::decode(Craft::$app->getInfo()->configMap) ?? [];
+
+        foreach ($configMap as &$filePath) {
+            $filePath = Craft::getAlias($filePath);
+        }
+
+        return $this->_configMap = $configMap;
     }
 
     /**