diff --git a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/SimpleJavaLibraryBuilder.java b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/SimpleJavaLibraryBuilder.java
index 50c936ac43360e..483b871d518c29 100644
--- a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/SimpleJavaLibraryBuilder.java
+++ b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/SimpleJavaLibraryBuilder.java
@@ -148,17 +148,21 @@ public BlazeJavacResult run(JavaLibraryBuildRequest build) throws Exception {
 
   public void buildJar(JavaLibraryBuildRequest build) throws IOException {
     JarCreator jar = new JarCreator(build.getOutputJar());
+    JacocoInstrumentationProcessor processor = null;
     try {
       jar.setNormalize(true);
       jar.setCompression(build.compressJar());
       jar.addDirectory(build.getClassDir());
       jar.setJarOwner(build.getTargetLabel(), build.getInjectingRuleKind());
-      JacocoInstrumentationProcessor processor = build.getJacocoInstrumentationProcessor();
+      processor = build.getJacocoInstrumentationProcessor();
       if (processor != null) {
         processor.processRequest(build, processor.isNewCoverageImplementation() ? jar : null);
       }
     } finally {
       jar.execute();
+      if (processor != null) {
+        processor.cleanup();
+      }
     }
   }
 
diff --git a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/instrumentation/JacocoInstrumentationProcessor.java b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/instrumentation/JacocoInstrumentationProcessor.java
index d3b37d257abf57..995c95d408d02f 100644
--- a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/instrumentation/JacocoInstrumentationProcessor.java
+++ b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/instrumentation/JacocoInstrumentationProcessor.java
@@ -37,24 +37,23 @@ public final class JacocoInstrumentationProcessor {
 
   public static JacocoInstrumentationProcessor create(List<String> args)
       throws InvalidCommandLineException {
-    if (args.size() < 2) {
+    if (args.size() < 1) {
       throw new InvalidCommandLineException(
-          "Number of arguments for Jacoco instrumentation should be 2+ (given "
+          "Number of arguments for Jacoco instrumentation should be 1+ (given "
               + args.size()
-              + ": metadataOutput metadataDirectory [filters*].");
+              + ": metadataOutput [filters*].");
     }
 
     // ignoring filters, they weren't used in the previous implementation
     // TODO(bazel-team): filters should be correctly handled
-    return new JacocoInstrumentationProcessor(args.get(1), args.get(0));
+    return new JacocoInstrumentationProcessor(args.get(0));
   }
 
-  private final String metadataDir;
+  private Path instrumentedClassesDirectory;
   private final String coverageInformation;
   private final boolean isNewCoverageImplementation;
 
-  private JacocoInstrumentationProcessor(String metadataDir, String coverageInfo) {
-    this.metadataDir = metadataDir;
+  private JacocoInstrumentationProcessor(String coverageInfo) {
     this.coverageInformation = coverageInfo;
     // This is part of the new Java coverage implementation where JacocoInstrumentationProcessor
     // receives a file that includes the relative paths of the uninstrumented Java files, instead
@@ -71,15 +70,10 @@ public boolean isNewCoverageImplementation() {
    * jacocoMetadataDir, to be zipped up in the output file jacocoMetadataOutput.
    */
   public void processRequest(JavaLibraryBuildRequest build, JarCreator jar) throws IOException {
-    // Clean up jacocoMetadataDir to be used by postprocessing steps. This is important when
-    // running JavaBuilder locally, to remove stale entries from previous builds.
-    if (metadataDir != null) {
-      Path workDir = Paths.get(metadataDir);
-      if (Files.exists(workDir)) {
-        recursiveRemove(workDir);
-      }
-      Files.createDirectories(workDir);
-    }
+    // Use a directory for coverage metadata  that is unique to each built jar. Avoids
+    // multiple threads performing read/write/delete actions on the instrumented classes directory.
+    instrumentedClassesDirectory = getMetadataDirRelativeToJar(build.getOutputJar());
+    Files.createDirectories(instrumentedClassesDirectory);
     if (jar == null) {
       jar = new JarCreator(coverageInformation);
     }
@@ -87,14 +81,26 @@ public void processRequest(JavaLibraryBuildRequest build, JarCreator jar) throws
     jar.setCompression(build.compressJar());
     Instrumenter instr = new Instrumenter(new OfflineInstrumentationAccessGenerator());
     instrumentRecursively(instr, build.getClassDir());
-    jar.addDirectory(metadataDir);
+    jar.addDirectory(instrumentedClassesDirectory);
     if (isNewCoverageImplementation) {
       jar.addEntry(coverageInformation, coverageInformation);
     } else {
       jar.execute();
+      cleanup();
+    }
+  }
+
+  public void cleanup() throws IOException {
+    if (Files.exists(instrumentedClassesDirectory)) {
+      recursiveRemove(instrumentedClassesDirectory);
     }
   }
 
+  // Return the path of the coverage metadata directory relative to the output jar path.
+  private static Path getMetadataDirRelativeToJar(Path outputJar) {
+    return outputJar.resolveSibling(outputJar + "-coverage-metadata");
+  }
+
   /**
    * Runs Jacoco instrumentation processor over all .class files recursively, starting with root.
    */
@@ -119,9 +125,9 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs)
             if (isNewCoverageImplementation) {
               Path absoluteUninstrumentedCopy = Paths.get(file + ".uninstrumented");
               uninstrumentedCopy =
-                  Paths.get(metadataDir).resolve(root.relativize(absoluteUninstrumentedCopy));
+                  instrumentedClassesDirectory.resolve(root.relativize(absoluteUninstrumentedCopy));
             } else {
-              uninstrumentedCopy = Paths.get(metadataDir).resolve(root.relativize(file));
+              uninstrumentedCopy = instrumentedClassesDirectory.resolve(root.relativize(file));
             }
             Files.createDirectories(uninstrumentedCopy.getParent());
             Files.move(file, uninstrumentedCopy);