diff --git a/app/infection-builds/infection.phar b/app/infection-builds/infection.phar
index a2548e1..cbff5de 100755
Binary files a/app/infection-builds/infection.phar and b/app/infection-builds/infection.phar differ
diff --git a/app/src/Infection/ConfigBuilder.php b/app/src/Infection/ConfigBuilder.php
index 3b331cd..7c571c9 100644
--- a/app/src/Infection/ConfigBuilder.php
+++ b/app/src/Infection/ConfigBuilder.php
@@ -38,6 +38,10 @@
 use function json_decode;
 use function json_encode;
 use const JSON_THROW_ON_ERROR;
+use function sprintf;
+use function str_starts_with;
+use function strlen;
+use function substr;
 
 /**
  * This class assumes that json was already validated by Infection's JSON schema.
@@ -56,10 +60,60 @@ final class ConfigBuilder
 
     private const TIMEOUT = 3;
 
+    private const NAMESPACE = 'Infected';
+
     public function build(string $userProvidedConfig): string
     {
+        $basicConfig = self::NOT_OVERRIDABLE_KEYS;
+        /** @var array{mutators?: array<string, bool>} $decodedOriginalConfig */
         $decodedOriginalConfig = json_decode($userProvidedConfig, true, JSON_THROW_ON_ERROR);
 
-        return (string) json_encode(self::NOT_OVERRIDABLE_KEYS + $decodedOriginalConfig);
+        if ($this->containsCustomMutator($decodedOriginalConfig['mutators'] ?? [])) {
+            $basicConfig['source']['excludes'] = $this->findCustomMutators($decodedOriginalConfig['mutators'] ?? []);
+        }
+
+        return (string) json_encode($basicConfig + $decodedOriginalConfig);
+    }
+
+    /**
+     * @param array<string, bool> $mutators
+     */
+    private function containsCustomMutator(array $mutators): bool
+    {
+        foreach ($mutators as $mutatorName => $mutatorConfig) {
+            if ($this->isCustomMutatorName($mutatorName)) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
+    /**
+     * @param array<string, bool> $mutators
+     *
+     * @return list<string>
+     */
+    private function findCustomMutators(array $mutators): array
+    {
+        $customMutatorNames = [];
+
+        foreach ($mutators as $mutatorName => $mutatorConfig) {
+            if ($this->isCustomMutatorName($mutatorName)) {
+                $customMutatorNames[] = substr($mutatorName, strlen($this->getStaticNamespace()));
+            }
+        }
+
+        return $customMutatorNames;
+    }
+
+    private function getStaticNamespace(): string
+    {
+        return sprintf('%s\\', self::NAMESPACE);
+    }
+
+    private function isCustomMutatorName(string $mutatorName): bool
+    {
+        return str_starts_with($mutatorName, $this->getStaticNamespace());
     }
 }
diff --git a/app/src/Infection/Runner.php b/app/src/Infection/Runner.php
index 746b5ef..83e34bc 100644
--- a/app/src/Infection/Runner.php
+++ b/app/src/Infection/Runner.php
@@ -45,7 +45,7 @@
 
 class Runner
 {
-    public const CURRENT_INFECTION_VERSION = '0.27.10';
+    public const CURRENT_INFECTION_VERSION = '0.29.1';
     public const CURRENT_PHPUNIT_VERSION = '10.5.10';
     public const CURRENT_PHP_VERSION = '8.2.13';
 
diff --git a/app/src/Json/infection-config-schema.json b/app/src/Json/infection-config-schema.json
index 104d60e..17f5a54 100644
--- a/app/src/Json/infection-config-schema.json
+++ b/app/src/Json/infection-config-schema.json
@@ -22,6 +22,9 @@
         "mutators": {
             "type": "object",
             "additionalProperties": false,
+            "patternProperties": {
+                "^[\\w]+(?:\\\\[\\w]+){1,}$": { "$ref": "#/definitions/default-mutator-config" }
+            },
             "description": "Contains the settings for different mutations and profiles",
             "properties": {
                 "global-ignore": {
diff --git a/app/tests/Unit/Infection/ConfigBuilderTest.php b/app/tests/Unit/Infection/ConfigBuilderTest.php
index f2af767..cf897f8 100644
--- a/app/tests/Unit/Infection/ConfigBuilderTest.php
+++ b/app/tests/Unit/Infection/ConfigBuilderTest.php
@@ -164,5 +164,33 @@ public static function provideConfigs(): Generator
                 ]
             ),
         ];
+
+        yield 'Custom mutators are automatically exluded from mutation' => [
+            <<<'JSON'
+{
+    "mutators": {"@default": false, "Infected\\CustomMutator1": true, "Infected\\CustomMutator2": true}
+}
+JSON
+            ,
+            [
+                'bootstrap' => './autoload.php',
+                'timeout' => 3,
+                'source' => [
+                    'directories' => ['src'],
+                    'excludes' => [
+                        'CustomMutator1',
+                        'CustomMutator2',
+                    ],
+                ],
+                'phpUnit' => ['customPath' => '../phpunit.phar'],
+                'tmpDir' => '.',
+                'logs' => ['json' => 'infection.log.json'],
+                'mutators' => [
+                    '@default' => false,
+                    'Infected\\CustomMutator1' => true,
+                    'Infected\\CustomMutator2' => true,
+                ],
+            ],
+        ];
     }
 }