diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 8232ce63f23..b8a7411a956 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -72,6 +72,7 @@ sourceSets {
 }
 
 allprojects {
+    apply plugin: 'java'
     targetCompatibility = 11
     sourceCompatibility = 11
 }
@@ -85,6 +86,13 @@ compileMinimumRuntimeJava {
     sourceCompatibility = 8
 }
 
+normalization {
+    runtimeClasspath {
+        // Ignore the embedded JAR as we track this separately below as a runtime dependency
+        ignore 'META-INF/*.jar'
+    }
+}
+
 jar {
     from sourceSets.minimumRuntime.output
     into('META-INF') {
@@ -143,6 +151,10 @@ if (project == rootProject) {
       mavenLocal()
     }
   }
+  dependencies {
+    // add this so the runtime classpath so Gradle will properly track it as a build runtime classpath input
+    runtimeOnly project('reaper')
+  }
   // only run tests as build-tools
   test.enabled = false
 }
diff --git a/buildSrc/reaper/build.gradle b/buildSrc/reaper/build.gradle
index 242dfcafaaa..8613d049da2 100644
--- a/buildSrc/reaper/build.gradle
+++ b/buildSrc/reaper/build.gradle
@@ -1,5 +1,3 @@
-apply plugin: 'java'
-
 jar {
     manifest {
         attributes 'Main-Class': 'org.elasticsearch.gradle.reaper.Reaper'