diff --git a/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilder.java b/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilder.java
index 59ba0c212e5bc3..1abe88ac56f929 100644
--- a/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilder.java
+++ b/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilder.java
@@ -264,6 +264,7 @@ CustomCommandLine.Builder createProtoCompilerCommandLine() throws MissingPrerequ
 
     // Add include maps
     addIncludeMapArguments(
+        !ruleContext.getFragment(ProtoConfiguration.class).generatedProtosInVirtualImports(),
         getOutputDirectory(ruleContext),
         result,
         areDepsStrict ? protoInfo.getStrictImportableProtoSourcesImportPaths() : null,
@@ -296,6 +297,9 @@ CustomCommandLine.Builder createProtoCompilerCommandLine() throws MissingPrerequ
                 .each(protosInExports)
                 .mapped(
                     new ExpandToPathFnWithImports(
+                        !ruleContext
+                            .getFragment(ProtoConfiguration.class)
+                            .generatedProtosInVirtualImports(),
                         getOutputDirectory(ruleContext),
                         protoInfo.getTransitiveProtoSourceRoots())));
       }
@@ -448,6 +452,9 @@ private static SpawnAction.Builder createActions(
         .setExecutable(compilerTarget)
         .addCommandLine(
             createCommandLineFromToolchains(
+                !ruleContext
+                    .getFragment(ProtoConfiguration.class)
+                    .generatedProtosInVirtualImports(),
                 toolchainInvocations,
                 getOutputDirectory(ruleContext),
                 protoInfo,
@@ -489,6 +496,7 @@ public static boolean arePublicImportsStrict(RuleContext ruleContext) {
    */
   @VisibleForTesting
   static CustomCommandLine createCommandLineFromToolchains(
+      boolean alwaysAddRepositoryPath,
       List<ToolchainInvocation> toolchainInvocations,
       String outputDirectory,
       ProtoInfo protoInfo,
@@ -537,6 +545,7 @@ static CustomCommandLine createCommandLineFromToolchains(
 
     // Add include maps
     addIncludeMapArguments(
+        alwaysAddRepositoryPath,
         outputDirectory,
         cmdLine,
         strictDeps == Deps.STRICT ? protoInfo.getStrictImportableProtoSourcesImportPaths() : null,
@@ -558,7 +567,9 @@ static CustomCommandLine createCommandLineFromToolchains(
                 .each(protoInfo.getExportedProtoSourcesImportPaths())
                 .mapped(
                     new ExpandToPathFnWithImports(
-                        outputDirectory, protoInfo.getExportedProtoSourceRoots())));
+                        alwaysAddRepositoryPath,
+                        outputDirectory,
+                        protoInfo.getExportedProtoSourceRoots())));
       }
     }
 
@@ -575,6 +586,7 @@ static CustomCommandLine createCommandLineFromToolchains(
 
   @VisibleForTesting
   static void addIncludeMapArguments(
+      boolean alwaysAddRepositoryPath,
       String outputDirectory,
       CustomCommandLine.Builder commandLine,
       @Nullable NestedSet<Pair<Artifact, String>> protosInDirectDependencies,
@@ -585,14 +597,18 @@ static void addIncludeMapArguments(
     // path when including other protos.
     commandLine.addAll(
         VectorArg.of(transitiveImports)
-            .mapped(new ExpandImportArgsFn(outputDirectory, directProtoSourceRoots)));
+            .mapped(
+                new ExpandImportArgsFn(
+                    alwaysAddRepositoryPath, outputDirectory, directProtoSourceRoots)));
     if (protosInDirectDependencies != null) {
       if (!protosInDirectDependencies.isEmpty()) {
         commandLine.addAll(
             "--direct_dependencies",
             VectorArg.join(":")
                 .each(protosInDirectDependencies)
-                .mapped(new ExpandToPathFnWithImports(outputDirectory, directProtoSourceRoots)));
+                .mapped(
+                    new ExpandToPathFnWithImports(
+                        alwaysAddRepositoryPath, outputDirectory, directProtoSourceRoots)));
 
       } else {
         // The proto compiler requires an empty list to turn on strict deps checking
@@ -636,10 +652,15 @@ private static String guessProtoPathUnderRoot(
   @AutoCodec
   @AutoCodec.VisibleForSerialization
   static final class ExpandImportArgsFn implements CapturingMapFn<Artifact> {
+    private final boolean alwaysAddRepositoryPath;
     private final String outputDirectory;
     private final NestedSet<String> directProtoSourceRoots;
 
-    public ExpandImportArgsFn(String outputDirectory, NestedSet<String> directProtoSourceRoots) {
+    public ExpandImportArgsFn(
+        boolean alwaysAddRepositoryPath,
+        String outputDirectory,
+        NestedSet<String> directProtoSourceRoots) {
+      this.alwaysAddRepositoryPath = alwaysAddRepositoryPath;
       this.outputDirectory = outputDirectory;
       this.directProtoSourceRoots = directProtoSourceRoots;
     }
@@ -651,24 +672,40 @@ public ExpandImportArgsFn(String outputDirectory, NestedSet<String> directProtoS
      */
     @Override
     public void expandToCommandLine(Artifact proto, Consumer<String> args) {
+      boolean repositoryPathAdded = !alwaysAddRepositoryPath;
+      String pathIgnoringRepository = getPathIgnoringRepository(proto);
+
       for (String directProtoSourceRoot : directProtoSourceRoots) {
         PathFragment sourceRootPath = PathFragment.create(directProtoSourceRoot);
         String arg = guessProtoPathUnderRoot(outputDirectory, sourceRootPath, proto);
         if (arg != null) {
+          if (arg.equals(pathIgnoringRepository)) {
+            repositoryPathAdded = true;
+          }
+
           args.accept("-I" + arg + "=" + proto.getExecPathString());
         }
       }
+
+      // TODO(lberki): This should really be removed. It's only there for backward compatibility.
+      if (!repositoryPathAdded) {
+        args.accept("-I" + getPathIgnoringRepository(proto) + "=" + proto.getExecPathString());
+      }
     }
   }
 
   @AutoCodec
   @AutoCodec.VisibleForSerialization
   static final class ExpandToPathFnWithImports implements CapturingMapFn<Pair<Artifact, String>> {
+    private final boolean alwaysAddRepositoryPath;
     private final String outputDirectory;
     private final NestedSet<String> directProtoSourceRoots;
 
     public ExpandToPathFnWithImports(
-        String outputDirectory, NestedSet<String> directProtoSourceRoots) {
+        boolean alwaysAddRepositoryPath,
+        String outputDirectory,
+        NestedSet<String> directProtoSourceRoots) {
+      this.alwaysAddRepositoryPath = alwaysAddRepositoryPath;
       this.outputDirectory = outputDirectory;
       this.directProtoSourceRoots = directProtoSourceRoots;
     }
@@ -678,17 +715,43 @@ public void expandToCommandLine(Pair<Artifact, String> proto, Consumer<String> a
       if (proto.second != null) {
         args.accept(proto.second);
       } else {
+        boolean repositoryPathAdded = !alwaysAddRepositoryPath;
+        String pathIgnoringRepository = getPathIgnoringRepository(proto.first);
+
         for (String directProtoSourceRoot : directProtoSourceRoots) {
           PathFragment sourceRootPath = PathFragment.create(directProtoSourceRoot);
           String arg = guessProtoPathUnderRoot(outputDirectory, sourceRootPath, proto.first);
           if (arg != null) {
+            if (arg.equals(pathIgnoringRepository)) {
+              repositoryPathAdded = true;
+            }
             args.accept(arg);
           }
         }
+
+        // TODO(lberki): This should really be removed. It's only there for backward compatibility.
+        if (!repositoryPathAdded) {
+          args.accept(pathIgnoringRepository);
+        }
       }
     }
   }
 
+  /**
+   * Gets the artifact's path relative to the root, ignoring the external repository the artifact is
+   * at. For example, <code>
+   * //a:b.proto --> a/b.proto
+   * {@literal @}foo//a:b.proto --> a/b.proto
+   * </code>
+   */
+  private static String getPathIgnoringRepository(Artifact artifact) {
+    return artifact
+        .getRootRelativePath()
+        .relativeTo(
+            artifact.getOwnerLabel().getPackageIdentifier().getRepository().getPathUnderExecRoot())
+        .toString();
+  }
+
   /**
    * Describes a toolchain and the value to replace for a $(OUT) that might appear in its
    * commandLine() (e.g., "bazel-out/foo.srcjar").
diff --git a/src/test/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilderTest.java b/src/test/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilderTest.java
index 914d86e0c10da4..5bc18c4fa80058 100644
--- a/src/test/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilderTest.java
+++ b/src/test/java/com/google/devtools/build/lib/rules/proto/ProtoCompileActionBuilderTest.java
@@ -104,6 +104,7 @@ public void commandLine_basic() throws Exception {
 
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             ImmutableList.of(
                 new ToolchainInvocation(
                     "dontcare_because_no_plugin", toolchainNoPlugin, "foo.srcjar"),
@@ -116,7 +117,7 @@ public void commandLine_basic() throws Exception {
                     artifact("//:dont-care", "import1.proto"),
                     artifact("//:dont-care", "import2.proto")),
 
-                /* transitiveProtoSourceRoots= */ NestedSetBuilder.create(Order.STABLE_ORDER, "."),
+                /* transitiveProtoSourceRoots= */ NestedSetBuilder.emptySet(STABLE_ORDER),
                 /* strictImportableProtoSourceRoots= */ NestedSetBuilder.create(
                     Order.STABLE_ORDER, "."),
                 /* strictImportableProtos= */ NestedSetBuilder.emptySet(STABLE_ORDER),
@@ -143,6 +144,7 @@ public void commandline_derivedArtifact() {
     // Verify that the command line contains the correct path to a generated protocol buffers.
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             /* toolchainInvocations= */ ImmutableList.of(),
             "bazel-out",
             protoInfo(
@@ -173,6 +175,7 @@ public void commandLine_strictDeps() throws Exception {
 
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             ImmutableList.of(new ToolchainInvocation("dontcare", toolchain, "foo.srcjar")),
             "bazel-out",
             protoInfo(
@@ -217,6 +220,7 @@ public void commandLine_exports() throws Exception {
 
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             ImmutableList.of(new ToolchainInvocation("dontcare", toolchain, "foo.srcjar")),
             "bazel-out",
             protoInfo(
@@ -225,9 +229,9 @@ public void commandLine_exports() throws Exception {
                     STABLE_ORDER,
                     artifact("//:dont-care", "import1.proto"),
                     artifact("//:dont-care", "import2.proto")),
-                /* transitiveProtoSourceRoots= */ NestedSetBuilder.create(Order.STABLE_ORDER, "."),
-                /* strictImportableProtoSourceRoots= */ NestedSetBuilder.create(
-                    Order.STABLE_ORDER, "."),
+
+                /* transitiveProtoSourceRoots= */ NestedSetBuilder.emptySet(STABLE_ORDER),
+                /* strictImportableProtoSourceRoots= */ NestedSetBuilder.emptySet(STABLE_ORDER),
                 /* strictImportableProtos= */ NestedSetBuilder.emptySet(STABLE_ORDER),
                 /* exportedProtos = */ NestedSetBuilder.create(
                     STABLE_ORDER,
@@ -253,6 +257,7 @@ public void commandLine_exports() throws Exception {
   public void otherParameters() throws Exception {
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             ImmutableList.of(),
             "bazel-out",
             protoInfo(
@@ -294,6 +299,7 @@ public String toString() {
 
     CustomCommandLine cmdLine =
         createCommandLineFromToolchains(
+            true,
             ImmutableList.of(new ToolchainInvocation("pluginName", toolchain, outReplacement)),
             "bazel-out",
             protoInfo(
@@ -339,6 +345,7 @@ public void exceptionIfSameName() throws Exception {
             IllegalStateException.class,
             () ->
                 createCommandLineFromToolchains(
+                    true,
                     ImmutableList.of(
                         new ToolchainInvocation("pluginName", toolchain1, "outReplacement"),
                         new ToolchainInvocation("pluginName", toolchain2, "outReplacement")),
@@ -455,6 +462,7 @@ private static Iterable<String> protoArgv(
     NestedSet<Artifact> transitiveImportsNestedSet =
         NestedSetBuilder.wrap(STABLE_ORDER, transitiveImports);
     ProtoCompileActionBuilder.addIncludeMapArguments(
+        true,
         "blaze-out",
         commandLine,
         protosInDirectDependenciesBuilder,
diff --git a/src/test/shell/bazel/bazel_proto_library_test.sh b/src/test/shell/bazel/bazel_proto_library_test.sh
index 88a6dabe68f386..2ae74816ec3420 100755
--- a/src/test/shell/bazel/bazel_proto_library_test.sh
+++ b/src/test/shell/bazel/bazel_proto_library_test.sh
@@ -384,6 +384,53 @@ EOF
 
 ############# TESTS #############
 
+function test_legacy_proto_library_include_well_known_protos() {
+  write_workspace ""
+
+  mkdir -p a
+  cat > a/BUILD <<EOF
+proto_library(
+  name="a",
+  srcs=["a.proto"],
+  deps=[":b"],
+)
+
+proto_library(
+  name="b",
+  srcs=["b.proto"],
+  deps=["@com_google_protobuf//:duration_proto"],
+)
+EOF
+
+  cat > a/a.proto <<EOF
+syntax = "proto3";
+
+package a;
+
+import "a/b.proto";
+
+message A {
+  int32 a = 1;
+  b.B b = 2;
+}
+EOF
+
+  cat > a/b.proto <<EOF
+syntax = "proto3";
+
+package b;
+
+import "google/protobuf/duration.proto";
+
+message B {
+ int32 b = 1;
+ google.protobuf.Duration timing = 2;
+}
+EOF
+
+  bazel build //a:a || fail "build failed"
+}
+
 function test_javainfo_proto_aspect() {
   write_workspace ""