diff --git a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkActionBuilder.java b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkActionBuilder.java
index a3d946f..cc89b69 100644
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkActionBuilder.java
+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkActionBuilder.java
@@ -742,7 +742,8 @@
 
     @Nullable Artifact thinltoParamFile = null;
     @Nullable Artifact thinltoMergedObjectFile = null;
-    PathFragment outputRootPath = output.getRootRelativePath();
+    PathFragment outputRootPath =
+        output.getOutputDirRelativePath(configuration.isSiblingRepositoryLayout());
     if (allowLtoIndexing && allLtoArtifacts != null) {
       // Create artifact for the file that the LTO indexing step will emit
       // object file names into for any that were included in the link as
@@ -1167,7 +1168,8 @@
       LinkArtifactFactory linkArtifactFactory) {
     ImmutableMap.Builder<Linkstamp, Artifact> mapBuilder = ImmutableMap.builder();
 
-    PathFragment outputBinaryPath = outputBinary.getRootRelativePath();
+    PathFragment outputBinaryPath =
+        outputBinary.getOutputDirRelativePath(configuration.isSiblingRepositoryLayout());
     PathFragment stampOutputDirectory =
         outputBinaryPath
             .getParentDirectory()
diff --git a/src/main/java/com/google/devtools/build/lib/rules/java/JavaCompilationHelper.java b/src/main/java/com/google/devtools/build/lib/rules/java/JavaCompilationHelper.java
index 509d3f0..1035277 100644
--- a/src/main/java/com/google/devtools/build/lib/rules/java/JavaCompilationHelper.java
+++ b/src/main/java/com/google/devtools/build/lib/rules/java/JavaCompilationHelper.java
@@ -454,7 +454,9 @@
   private Artifact turbineOutput(Artifact classJar, String newExtension) {
     return getAnalysisEnvironment()
         .getDerivedArtifact(
-            FileSystemUtils.replaceExtension(classJar.getRootRelativePath(), newExtension),
+            FileSystemUtils.replaceExtension(
+                classJar.getOutputDirRelativePath(getConfiguration().isSiblingRepositoryLayout()),
+                newExtension),
             classJar.getRoot());
   }