diff --git a/buildSrc/call-site-instrumentation-plugin/build.gradle.kts b/buildSrc/call-site-instrumentation-plugin/build.gradle.kts
index 82b9466d1bb..80097f55629 100644
--- a/buildSrc/call-site-instrumentation-plugin/build.gradle.kts
+++ b/buildSrc/call-site-instrumentation-plugin/build.gradle.kts
@@ -1,3 +1,7 @@
+import com.github.jengelman.gradle.plugins.shadow.transformers.ApacheLicenseResourceTransformer
+import com.github.jengelman.gradle.plugins.shadow.transformers.ApacheNoticeResourceTransformer
+import org.gradle.api.file.DuplicatesStrategy.INCLUDE
+
 plugins {
   java
   id("com.diffplug.spotless") version "8.4.0"
@@ -69,11 +73,11 @@ tasks {
   }
 
   shadowJar {
-    duplicatesStrategy = DuplicatesStrategy.FAIL
-    // Let's skip license/notice since this jar's only use is during build
-    filesMatching(listOf("META-INF/LICENSE*", "META-INF/NOTICE*")) {
-      duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-    }
+    duplicatesStrategy = INCLUDE
+    transform<ApacheLicenseResourceTransformer>()
+    transform<ApacheNoticeResourceTransformer>()
+    failOnDuplicateEntries = true
+
     manifest {
       attributes(mapOf("Main-Class" to "datadog.trace.plugin.csi.PluginApplication"))
     }
diff --git a/dd-java-agent/build.gradle b/dd-java-agent/build.gradle
index 38b686c76ab..a55735f7a47 100644
--- a/dd-java-agent/build.gradle
+++ b/dd-java-agent/build.gradle
@@ -1,4 +1,7 @@
+import static org.gradle.api.file.DuplicatesStrategy.INCLUDE
+
 import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
+import com.github.jengelman.gradle.plugins.shadow.transformers.PreserveFirstFoundResourceTransformer
 import java.util.concurrent.atomic.AtomicBoolean
 import java.util.jar.JarFile
 
@@ -83,21 +86,19 @@ def generalShadowJarConfig(ShadowJar shadowJarTask) {
     mergeServiceFiles()
     addMultiReleaseAttribute = false
 
-    duplicatesStrategy = DuplicatesStrategy.FAIL
-    // Service descriptors are intentionally merged by mergeServiceFiles(); let
-    // duplicate service entries reach that transformer instead of failing first.
-    filesMatching('META-INF/services/**') {
-      duplicatesStrategy = DuplicatesStrategy.INCLUDE
-    }
-    // Vendored dependencies often repeat license/notice metadata. Keep one copy
-    // while still failing on unexpected duplicate runtime resources and classes.
-    filesMatching([
-      'META-INF/LICENSE*',
-      'META-INF/NOTICE*',
-      'META-INF/AL2.0',
-      'META-INF/LGPL2.1',
-    ]) {
-      duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+    // Allow duplicate to merge service files
+    duplicatesStrategy = INCLUDE
+    // Ensure there is no duplicate in the final jar after resource transformer applied
+    failOnDuplicateEntries = true
+
+    // Vendored dependencies repeat license/notice metadata; keep a single copy
+    transform(PreserveFirstFoundResourceTransformer) {
+      it.include(
+        'META-INF/LICENSE*',
+        'META-INF/NOTICE*',
+        'META-INF/AL2.0',
+        'META-INF/LGPL2.1',
+        )
     }
 
     // Remove some cruft from the final jar.