diff --git a/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCommon.java b/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCommon.java
index 1463bbfc341129..cbeeaa264809d0 100644
--- a/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCommon.java
+++ b/src/main/java/com/google/devtools/build/lib/rules/proto/ProtoCommon.java
@@ -19,6 +19,7 @@
 import static com.google.devtools.build.lib.syntax.Type.STRING;
 
 import com.google.common.annotations.VisibleForTesting;
+import com.google.common.base.Optional;
 import com.google.common.collect.ImmutableList;
 import com.google.devtools.build.lib.actions.Artifact;
 import com.google.devtools.build.lib.actions.ArtifactRoot;
@@ -136,10 +137,13 @@ static NestedSet<Artifact> computeDependenciesDescriptorSets(RuleContext ruleCon
    * <p>Assumes {@code currentProtoSourceRoot} is the same as the package name.
    */
   private static NestedSet<String> computeTransitiveProtoSourceRoots(
-      RuleContext ruleContext, String currentProtoSourceRoot) {
+      RuleContext ruleContext, Optional<String> currentProtoSourceRoot) {
     NestedSetBuilder<String> protoPath = NestedSetBuilder.stableOrder();
 
-    protoPath.add(currentProtoSourceRoot);
+    if (currentProtoSourceRoot.isPresent()) {
+      protoPath.add(currentProtoSourceRoot.get());
+    }
+
     for (ProtoInfo provider :
         ruleContext.getPrerequisites("deps", Mode.TARGET, ProtoInfo.PROVIDER)) {
       protoPath.addTransitive(provider.getTransitiveProtoSourceRoots());
@@ -159,11 +163,11 @@ private static NestedSet<String> computeTransitiveProtoSourceRoots(
   static final class Library {
     private final ImmutableList<Artifact> sources;
     private final ImmutableList<Pair<Artifact, String>> importPathSourcePair;
-    private final String sourceRoot;
+    private final Optional<String> sourceRoot;
 
     Library(
         ImmutableList<Artifact> sources,
-        String sourceRoot,
+        Optional<String> sourceRoot,
         ImmutableList<Pair<Artifact, String>> importPathSourcePair) {
       this.sources = sources;
       this.sourceRoot = sourceRoot;
@@ -178,7 +182,7 @@ public ImmutableList<Pair<Artifact, String>> getImportPathSourcePair() {
       return importPathSourcePair;
     }
 
-    public String getSourceRoot() {
+    public Optional<String> getSourceRoot() {
       return sourceRoot;
     }
   }
@@ -201,22 +205,38 @@ private static Library getProtoSourceRoot(
       return null;
     }
 
-    // This is the same as getPackageIdentifier().getPathUnderExecRoot() due to the check above for
-    // protoSourceRoot == package name, but it's a bit more future-proof.
-    String result =
-        ruleContext
-            .getLabel()
-            .getPackageIdentifier()
-            .getRepository()
-            .getPathUnderExecRoot()
-            .getRelative(protoSourceRoot)
-            .getPathString();
+    boolean hasNonGeneratedSources = false;
+    for (Artifact artifact : directSources) {
+      if (artifact.isSourceArtifact()) {
+        hasNonGeneratedSources = true;
+        break;
+      }
+    }
+
+    String sourceRoot = "";
+    // Otherwise, we'll direct the proto compiler to the source files using -Ifoo=bar arguments.
+    // Then let's not spam the command line.
+    if (hasNonGeneratedSources) {
+      // This is the same as getPackageIdentifier().getPathUnderExecRoot() due to the check above
+      // for protoSourceRoot == package name, but it's a bit more future-proof.
+      sourceRoot =
+          ruleContext
+              .getLabel()
+              .getPackageIdentifier()
+              .getRepository()
+              .getPathUnderExecRoot()
+              .getRelative(protoSourceRoot)
+              .getPathString();
+    }
 
     ImmutableList.Builder<Pair<Artifact, String>> builder = ImmutableList.builder();
     for (Artifact protoSource : directSources) {
       builder.add(new Pair<Artifact, String>(protoSource, null));
     }
-    return new Library(directSources, result.isEmpty() ? "." : result, builder.build());
+    return new Library(
+        directSources,
+        sourceRoot.isEmpty() ? Optional.absent() : Optional.of(sourceRoot),
+        builder.build());
   }
 
   private static PathFragment getPathFragmentAttribute(
@@ -327,7 +347,7 @@ private static Library createVirtualImportDirectoryMaybe(
             .getExecPath()
             .getRelative(sourceRootPath)
             .getPathString();
-    return new Library(symlinks.build(), sourceRoot, protoSourceImportPair.build());
+    return new Library(symlinks.build(), Optional.of(sourceRoot), protoSourceImportPair.build());
   }
 
   private static Pair<PathFragment, Artifact> computeImports(
@@ -361,9 +381,11 @@ private static Pair<PathFragment, Artifact> computeImports(
    * <p>Assumes {@code currentProtoSourceRoot} is the same as the package name.
    */
   private static NestedSet<String> getProtoSourceRootsOfAttribute(
-      RuleContext ruleContext, String currentProtoSourceRoot, String attributeName) {
+      RuleContext ruleContext, Optional<String> currentProtoSourceRoot, String attributeName) {
     NestedSetBuilder<String> protoSourceRoots = NestedSetBuilder.stableOrder();
-    protoSourceRoots.add(currentProtoSourceRoot);
+    if (currentProtoSourceRoot.isPresent()) {
+      protoSourceRoots.add(currentProtoSourceRoot.get());
+    }
 
     for (ProtoInfo provider :
         ruleContext.getPrerequisites(attributeName, Mode.TARGET, ProtoInfo.PROVIDER)) {
@@ -380,7 +402,7 @@ private static NestedSet<String> getProtoSourceRootsOfAttribute(
    * <p>Assumes {@code currentProtoSourceRoot} is the same as the package name.
    */
   private static NestedSet<String> computeStrictImportableProtoSourceRoots(
-      RuleContext ruleContext, String currentProtoSourceRoot) {
+      RuleContext ruleContext, Optional<String> currentProtoSourceRoot) {
     return getProtoSourceRootsOfAttribute(ruleContext, currentProtoSourceRoot, "deps");
   }
 
@@ -391,7 +413,7 @@ private static NestedSet<String> computeStrictImportableProtoSourceRoots(
    * <p>Assumes {@code currentProtoSourceRoot} is the same as the package name.
    */
   private static NestedSet<String> computeExportedProtoSourceRoots(
-      RuleContext ruleContext, String currentProtoSourceRoot) {
+      RuleContext ruleContext, Optional<String> currentProtoSourceRoot) {
     return getProtoSourceRootsOfAttribute(ruleContext, currentProtoSourceRoot, "exports");
   }
 
@@ -490,7 +512,7 @@ public static ProtoInfo createProtoInfo(RuleContext ruleContext) {
     ProtoInfo protoInfo =
         new ProtoInfo(
             library.getSources(),
-            library.getSourceRoot(),
+            library.getSourceRoot().or("."),
             transitiveProtoSources,
             transitiveProtoSourceRoots,
             strictImportableProtosForDependents,
diff --git a/src/test/java/com/google/devtools/build/lib/rules/proto/BazelProtoLibraryTest.java b/src/test/java/com/google/devtools/build/lib/rules/proto/BazelProtoLibraryTest.java
index 225134e5187910..447763bf4daeb5 100644
--- a/src/test/java/com/google/devtools/build/lib/rules/proto/BazelProtoLibraryTest.java
+++ b/src/test/java/com/google/devtools/build/lib/rules/proto/BazelProtoLibraryTest.java
@@ -340,8 +340,34 @@ public void testProtoSourceRootWithDeps() throws Exception {
     );
     ConfiguredTarget protoTarget = getConfiguredTarget("//x/foo:withdeps");
     ProtoInfo sourcesProvider = protoTarget.get(ProtoInfo.PROVIDER);
-    assertThat(sourcesProvider.getTransitiveProtoSourceRoots())
-        .containsExactly("x/foo", "x/bar", ".");
+    assertThat(sourcesProvider.getTransitiveProtoSourceRoots()).containsExactly("x/foo", "x/bar");
+  }
+
+  @Test
+  public void testExternalRepoWithGeneratedProto() throws Exception {
+    if (!isThisBazel()) {
+      return;
+    }
+
+    FileSystemUtils.appendIsoLatin1(
+        scratch.resolve("WORKSPACE"), "local_repository(name = 'foo', path = '/foo')");
+    invalidatePackages();
+
+    scratch.file("/foo/WORKSPACE");
+    scratch.file(
+        "/foo/x/BUILD",
+        "proto_library(name='x', srcs=['generated.proto'])",
+        "genrule(name='g', srcs=[], outs=['generated.proto'], cmd='')");
+
+    scratch.file("a/BUILD", "proto_library(name='a', srcs=['a.proto'], deps=['@foo//x:x'])");
+
+    ConfiguredTarget a = getConfiguredTarget("//a:a");
+    ProtoInfo aInfo = a.get(ProtoInfo.PROVIDER);
+    assertThat(aInfo.getTransitiveProtoSourceRoots()).isEmpty();
+
+    ConfiguredTarget x = getConfiguredTarget("@foo//x:x");
+    ProtoInfo xInfo = x.get(ProtoInfo.PROVIDER);
+    assertThat(xInfo.getTransitiveProtoSourceRoots()).isEmpty();
   }
 
   @Test