diff --git a/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy b/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
index 35b656d6..2e6f2510 100644
--- a/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
@@ -604,7 +604,7 @@ public abstract class GenerateProtoTask extends DefaultTask {
 
     // The source directory designated from sourceSet may not actually exist on disk.
     // "include" it only when it exists, so that Gradle and protoc won't complain.
-    List<String> dirs = (sourceDirs + includeDirs).filter { File it -> it.exists() }*.path
+    List<String> dirs = includeDirs.filter { File it -> it.exists() }*.path
         .collect { "-I${it}".toString() }
     logger.debug "ProtobufCompile using directories ${dirs}"
     logger.debug "ProtobufCompile using files ${protoFiles}"
diff --git a/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy b/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
index 60840cb1..82b18d67 100644
--- a/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
@@ -248,7 +248,7 @@ class ProtobufPlugin implements Plugin<Project> {
       Provider<ProtobufExtract> extractIncludeProtosTask = setupExtractIncludeProtosTask(
           sourceSet.name, compileProtoPath, sourceSet.compileClasspath)
       Provider<GenerateProtoTask> generateProtoTask = addGenerateProtoTask(
-          sourceSet.name, protoSrcDirSet.sourceDirectories, project.files(extractProtosTask),
+          sourceSet.name, protoSrcDirSet, project.files(extractProtosTask),
           extractIncludeProtosTask) {
         it.sourceSet = sourceSet
         it.doneInitializing()
@@ -320,9 +320,8 @@ class ProtobufPlugin implements Plugin<Project> {
           setupExtractIncludeProtosTask(variant.name, classPathConfig, testClassPathConfig)
 
       // GenerateProto task, one per variant (compilation unit).
-      FileCollection sourceDirs = project.files(project.providers.provider {
-          variant.sourceSets.collect { it.proto.sourceDirectories }
-      })
+      SourceDirectorySet sourceDirs = project.objects.sourceDirectorySet(variant.name, "AllSourceSets")
+      variant.sourceSets.forEach { sourceDirs.source(it.proto) }
       FileCollection extractProtosDirs = project.files(project.providers.provider {
         variant.sourceSets.collect {
           project.files(project.tasks.named(getExtractProtosTaskName(it.name)))
@@ -367,9 +366,10 @@ class ProtobufPlugin implements Plugin<Project> {
      * compiled. For Java it's the sourceSet that sourceSetOrVariantName stands
      * for; for Android it's the collection of sourceSets that the variant includes.
      */
+    @SuppressWarnings(["UnnecessaryObjectReferences"]) // suppress a lot of it.doLogic in task registration block
     private Provider<GenerateProtoTask> addGenerateProtoTask(
         String sourceSetOrVariantName,
-        FileCollection sourceDirs,
+        SourceDirectorySet protoSourceSet,
         FileCollection extractProtosDirs,
         Provider<ProtobufExtract> extractIncludeProtosTask,
         Action<GenerateProtoTask> configureAction) {
@@ -381,8 +381,10 @@ class ProtobufPlugin implements Plugin<Project> {
       return project.tasks.register(generateProtoTaskName, GenerateProtoTask) {
         it.description = "Compiles Proto source for '${sourceSetOrVariantName}'".toString()
         it.outputBaseDir = outDir
-        it.addSourceDirs(sourceDirs)
+        it.addSourceDirs(protoSourceSet)
+        it.addIncludeDir(protoSourceSet.sourceDirectories)
         it.addSourceDirs(extractProtosDirs)
+        it.addIncludeDir(extractProtosDirs)
         it.addIncludeDir(project.files(extractIncludeProtosTask))
         configureAction.execute(it)
       }
diff --git a/src/test/groovy/com/google/protobuf/gradle/ProtobufJavaPluginTest.groovy b/src/test/groovy/com/google/protobuf/gradle/ProtobufJavaPluginTest.groovy
index 58c72b59..451a6610 100644
--- a/src/test/groovy/com/google/protobuf/gradle/ProtobufJavaPluginTest.groovy
+++ b/src/test/groovy/com/google/protobuf/gradle/ProtobufJavaPluginTest.groovy
@@ -35,6 +35,23 @@ class ProtobufJavaPluginTest extends Specification {
     assert project.tasks.extractTestProto instanceof ProtobufExtract
   }
 
+  void "test generate proto task sources should include only *.proto files"() {
+    given: "a project with readme file in proto source directory"
+    Project project = setupBasicProject()
+    project.file("src/main/proto").mkdirs()
+    project.file("src/main/proto/messages.proto") << "syntax = \"proto3\";"
+    project.file("src/main/proto/README.md") << "Hello World"
+
+    when: "project evaluated"
+    project.evaluate()
+
+    then: "it contains only *.proto files"
+    assert Objects.equals(
+      project.tasks.generateProto.sourceDirs.asFileTree.files,
+      [project.file("src/main/proto/messages.proto")] as Set<File>
+    )
+  }
+
   void "testCustom sourceSet should get its own GenerateProtoTask"() {
     given: "a basic project with java and com.google.protobuf"
     Project project = setupBasicProject()
diff --git a/testProjectAndroidBase/src/main/proto/README.md b/testProjectAndroidBase/src/main/proto/README.md
new file mode 100644
index 00000000..557db03d
--- /dev/null
+++ b/testProjectAndroidBase/src/main/proto/README.md
@@ -0,0 +1 @@
+Hello World
diff --git a/testProjectAndroidBase/src/test/proto/README.md b/testProjectAndroidBase/src/test/proto/README.md
new file mode 100644
index 00000000..557db03d
--- /dev/null
+++ b/testProjectAndroidBase/src/test/proto/README.md
@@ -0,0 +1 @@
+Hello World
diff --git a/testProjectBase/src/main/proto/README.md b/testProjectBase/src/main/proto/README.md
new file mode 100644
index 00000000..557db03d
--- /dev/null
+++ b/testProjectBase/src/main/proto/README.md
@@ -0,0 +1 @@
+Hello World
diff --git a/testProjectBase/src/test/proto/README.md b/testProjectBase/src/test/proto/README.md
new file mode 100644
index 00000000..557db03d
--- /dev/null
+++ b/testProjectBase/src/test/proto/README.md
@@ -0,0 +1 @@
+Hello World