diff --git a/bazel/src/main/java/com/google/api/codegen/bazel/ApisVisitor.java b/bazel/src/main/java/com/google/api/codegen/bazel/ApisVisitor.java
index 5f4bca5..0fcdb7c 100644
--- a/bazel/src/main/java/com/google/api/codegen/bazel/ApisVisitor.java
+++ b/bazel/src/main/java/com/google/api/codegen/bazel/ApisVisitor.java
@@ -135,6 +135,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
     String dirStr = dir.toString();
     ApiVersionedDir bp = bazelApiVerPackages.get(dirStr);
     BazelBuildFileTemplate template = null;
+    boolean preserveExisting = false;
     String tmplType = "";
     if (bp.getProtoPackage() != null) {
       boolean isGapicLibrary =
@@ -150,6 +151,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
     } else if (bp.getServiceYamlPath() != null) {
       template = this.rootApiTempl;
       tmplType = "API_ROOT";
+      preserveExisting = !overwrite;
     }
 
     if (template == null) {
@@ -159,6 +161,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
     String rootDirStr = srcDir.toString();
     String outDirPath = destDir.toString() + dirStr.substring(rootDirStr.length());
     File outDir = new File(outDirPath);
+    Path outFilePath = Paths.get(outDir.toString(), "BUILD.bazel");
 
     if (!outDir.exists()) {
       if (!outDir.mkdirs()) {
@@ -167,11 +170,19 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
       }
     }
 
+    // Currently we avoid overwriting existing root api build files. This is to
+    // preserve such files that may contain manually-added rules for generating
+    // Ruby wrappers, which we cannot generate yet. In the future, we should
+    // expand this tool to generate those rules.
+    if (preserveExisting && outFilePath.toFile().exists()) {
+      return FileVisitResult.CONTINUE;
+    }
+
     System.out.println(
         "Write File [" + tmplType + "]: " + outDir.toString() + File.separator + "BUILD.bazel");
     try {
       BazelBuildFileView bpv = new BazelBuildFileView(bp);
-      fileWriter.write(Paths.get(outDir.toString(), "BUILD.bazel"), template.expand(bpv));
+      fileWriter.write(outFilePath, template.expand(bpv));
     } catch (RuntimeException ex) {
       ex.printStackTrace();
     }
diff --git a/bazel/src/test/java/com/google/api/codegen/bazel/BuildFileGeneratorTest.java b/bazel/src/test/java/com/google/api/codegen/bazel/BuildFileGeneratorTest.java
index 6548569..8fe105e 100644
--- a/bazel/src/test/java/com/google/api/codegen/bazel/BuildFileGeneratorTest.java
+++ b/bazel/src/test/java/com/google/api/codegen/bazel/BuildFileGeneratorTest.java
@@ -15,6 +15,7 @@
 package com.google.api.codegen.bazel;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -72,10 +73,13 @@ public void testGenerateBuildFiles_legacyJavaLanguageOverrides() throws IOExcept
 
   @Test
   public void testRegeneration() throws IOException, InterruptedException {
-    // In this test we run the generator twice, changing the generated
-    // google/example/library/v1/BUILD.bazel
-    // after the first run, and verifying that some changed values are preserved
-    // (and some are not).
+    // In this test we run the generator multiple times, changing the generated
+    // google/example/library/v1/BUILD.bazel (i.e. GAPIC_VERSIONED) and
+    // google/example/library/BUILD.bazel (i.e. API_ROOT) after the first run.
+    // In the GAPIC_VERSIONED file, we verify that some changed values are
+    // preserved and others are not. In the API_ROOT file, we verify that all
+    // modifications are preserved. Finally, we rerun the generator with
+    // --overwrite to ensure that it properly overwrites all changes.
     Path tempDirPath = getTemporaryDirectory();
 
     // I'm lazy, so let's just "cp -r" stuff.
@@ -134,6 +138,10 @@ public void testRegeneration() throws IOException, InterruptedException {
 
     buildozer.commit();
 
+    // Change the content in google/example/library/BUILD.bazel
+    String changedRootContent = "# Hello\n";
+    Files.write(Paths.get(rootBuildFilePath), changedRootContent.getBytes(StandardCharsets.UTF_8));
+
     // Run the generator again
     new BuildFileGenerator()
         .generateBuildFiles(args.createApisVisitor(null, tempDirPath.toString()));
@@ -160,6 +168,9 @@ public void testRegeneration() throws IOException, InterruptedException {
     Assert.assertEquals(
         "library_example_grpc_service_config.json",
         buildozer.getAttribute(gapicBuildFilePath, "library_nodejs_gapic", "grpc_service_config"));
+    
+    // Check that the changed root file is preserved
+    Assert.assertEquals(changedRootContent, ApisVisitor.readFile(rootBuildFilePath));
 
     // Now run with overwrite and verify it actually ignores all the changes
     ArgsParser argsOverwrite =