diff --git a/.github/workflows/native-tests.yml b/.github/workflows/native-tests.yml
index 7b7898896..a099aaafc 100644
--- a/.github/workflows/native-tests.yml
+++ b/.github/workflows/native-tests.yml
@@ -19,5 +19,4 @@ jobs:
           sha256: 96f6f1f416d868b78addd22746eefc7f4bf7820c6a3afa392a9f653f708c1644
           working_directory: .mise/envs/native
       - name: Run native tests
-        working-directory: .mise/envs/native
-        run: mise native-test
+        run: mise //.mise/envs/native:native-test
diff --git a/.mise/envs/native/mise.toml b/.mise/envs/native/mise.toml
index 594ec3d80..b64367044 100644
--- a/.mise/envs/native/mise.toml
+++ b/.mise/envs/native/mise.toml
@@ -2,6 +2,9 @@
 java = "oracle-graalvm-25.0.1"
 
 [tasks.native-test]
-depends = "build"
-run = "../../mvnw test -PnativeTest"
-dir = "../../../integration-tests/it-spring-boot-smoke-test"
+depends = "//:build"
+# Native Test uses Surefire, so explicitly select the Failsafe-named test class.
+run = '''
+cd "$MISE_MONOREPO_ROOT/integration-tests/it-spring-boot-smoke-test"
+"$MISE_MONOREPO_ROOT/mvnw" test -PnativeTest -Dtest=ApplicationIT
+'''
diff --git a/integration-tests/it-spring-boot-smoke-test/pom.xml b/integration-tests/it-spring-boot-smoke-test/pom.xml
index e27ae713e..6c0f92357 100644
--- a/integration-tests/it-spring-boot-smoke-test/pom.xml
+++ b/integration-tests/it-spring-boot-smoke-test/pom.xml
@@ -91,6 +91,19 @@
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-maven-plugin</artifactId>
       </plugin>
+      <!-- Run after package so reactor dependencies resolve to their shaded artifacts. -->
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-failsafe-plugin</artifactId>
+        <executions>
+          <execution>
+            <goals>
+              <goal>integration-test</goal>
+              <goal>verify</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
 
diff --git a/integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationTest.java b/integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationIT.java
similarity index 92%
rename from integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationTest.java
rename to integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationIT.java
index c56634624..43f389482 100644
--- a/integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationTest.java
+++ b/integration-tests/it-spring-boot-smoke-test/src/test/java/io/prometheus/metrics/it/springboot/ApplicationIT.java
@@ -17,7 +17,13 @@
 import org.springframework.boot.test.context.SpringBootTest;
 
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.DEFINED_PORT)
-class ApplicationTest {
+class ApplicationIT {
+  @Test
+  void testUsesShadedProtobufRuntime() {
+    assertThat(Metrics.MetricFamily.class.getSuperclass().getName())
+        .startsWith("io.prometheus.metrics.shaded.com_google_protobuf_");
+  }
+
   @Test
   void testPrometheusProtobufFormat() throws IOException {
     ExporterTest.Response response =
diff --git a/mise.toml b/mise.toml
index 021e0921c..698fc7ec3 100644
--- a/mise.toml
+++ b/mise.toml
@@ -1,3 +1,8 @@
+monorepo_root = true
+
+[monorepo]
+config_roots = [".mise/envs/*"]
+
 [tools]
 "aqua:grafana/gcx" = "v1.1.0"
 "aqua:grafana/oats" = "0.10.0"