diff --git a/README.md b/README.md
index 06f92161..290e9e8d 100644
--- a/README.md
+++ b/README.md
@@ -315,12 +315,10 @@ task.plugins {
 
 ```gradle
 protobuf {
-  generatedFilesBaseDir = "$projectDir/generated"
-
   generateProtoTasks {
     all().each { task ->
       task.builtins {
-        // Generates Python code in the output folder:
+        // Generates Python code
         python { }
 
         // If you wish to avoid generating Java files:
@@ -410,7 +408,7 @@ protobuf {
 ```gradle
 { task ->
   // If true, will generate a descriptor_set.desc file under
-  // $generatedFilesBaseDir/$sourceSet. Default is false.
+  // task.outputBaseDir. Default is false.
   // See --descriptor_set_out in protoc documentation about what it is.
   task.generateDescriptorSet = true
 
@@ -430,19 +428,11 @@ protobuf {
 
 #### Change where files are generated
 
-By default generated Java files are under
-``$generatedFilesBaseDir/$sourceSet/$builtinPluginName``, where
-``$generatedFilesBaseDir`` is ``$buildDir/generated/source/proto`` by default,
-and is configurable. E.g.,
-
-```gradle
-protobuf {
-  ...
-  generatedFilesBaseDir = "$projectDir/src/generated"
-}
-```
+Generated files are under `task.outputBaseDir` with a subdirectory per
+builtin and plugin. This produces a folder structure of
+``$buildDir/generated/source/proto/$sourceSet/$builtinPluginName``.
 
-The subdirectory name, which is by default ``$builtinPluginName``, can also be
+The subdirectory name, which is by default ``$builtinPluginName``, can be
 changed by setting the ``outputSubDir`` property in the ``builtins`` or
 ``plugins`` block of a task configuration within ``generateProtoTasks`` block
 (see previous section). E.g.,
@@ -451,8 +441,7 @@ changed by setting the ``outputSubDir`` property in the ``builtins`` or
 { task ->
   task.plugins {
     grpc {
-      // Write the generated files under
-      // "$generatedFilesBaseDir/$sourceSet/grpcjava"
+      // Use subdirectory 'grpcjava' instead of the default 'grpc'
       outputSubDir = 'grpcjava'
     }
   }
@@ -521,29 +510,6 @@ This plugin integrates with the ``idea`` plugin and automatically
 registers the proto files and generated Java code as sources.
 
 
-```gradle
-apply plugin: 'idea'
-
-protobuf {
-    ...
-    generatedFilesBaseDir = "$projectDir/gen"
-}
-
-clean {
-    delete protobuf.generatedFilesBaseDir
-}
-
-idea {
-    module {
-        // proto files and generated Java files are automatically added as
-        // source dirs.
-        // If you have additional sources, add them here:
-        sourceDirs += file("/path/to/other/sources");
-    }
-}
-```
-
-
 ## Testing the plugin
 
 ``testProject*`` are testing projects that uses this plugin to compile
diff --git a/config/codenarc/codenarc.xml b/config/codenarc/codenarc.xml
index 17af312e..12e743c1 100644
--- a/config/codenarc/codenarc.xml
+++ b/config/codenarc/codenarc.xml
@@ -82,9 +82,13 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   <ruleset-ref path='rulesets/unnecessary.xml'>
     <exclude name="UnnecessaryCollectCall"/>
     <exclude name="UnnecessaryGetter"/>
+
     <exclude name="UnnecessaryGString"/>
     <exclude name="UnnecessarySetter"/>
     <exclude name="UnnecessaryPublicModifier"/>
     <exclude name="UnnecessaryReturnKeyword"/>
+
+    <!-- Poor suggestion when using static typing -->
+    <exclude name="UnnecessaryObjectReferences"/>
   </ruleset-ref>
 </ruleset>
diff --git a/src/main/groovy/com/google/protobuf/gradle/CopyActionFacade.java b/src/main/groovy/com/google/protobuf/gradle/CopyActionFacade.java
index 804f3aa7..64e08389 100644
--- a/src/main/groovy/com/google/protobuf/gradle/CopyActionFacade.java
+++ b/src/main/groovy/com/google/protobuf/gradle/CopyActionFacade.java
@@ -33,8 +33,11 @@
 import org.gradle.api.Action;
 import org.gradle.api.Project;
 import org.gradle.api.file.CopySpec;
+import org.gradle.api.file.DeleteSpec;
 import org.gradle.api.file.FileSystemOperations;
+import org.gradle.api.model.ObjectFactory;
 import org.gradle.api.tasks.WorkResult;
+import org.gradle.util.GradleVersion;
 
 import javax.inject.Inject;
 
@@ -46,6 +49,18 @@
 @CompileStatic
 interface CopyActionFacade {
     WorkResult copy(Action<? super CopySpec> var1);
+    WorkResult delete(Action<? super DeleteSpec> action);
+
+    @CompileStatic
+    final class Loader {
+        public static CopyActionFacade create(Project project, ObjectFactory objectFactory) {
+            if (GradleVersion.current().compareTo(GradleVersion.version("6.0")) >= 0) {
+                // Use object factory to instantiate as that will inject the necessary service.
+                return objectFactory.newInstance(CopyActionFacade.FileSystemOperationsBased.class);
+            }
+            return new CopyActionFacade.ProjectBased(project);
+        }
+    }
 
     @CompileStatic
     class ProjectBased implements CopyActionFacade {
@@ -59,6 +74,11 @@ public ProjectBased(Project project) {
         public WorkResult copy(Action<? super CopySpec> action) {
             return project.copy(action);
         }
+
+        @Override
+        public WorkResult delete(Action<? super DeleteSpec> action) {
+            return project.delete(action);
+        }
     }
 
     @CompileStatic
@@ -70,5 +90,10 @@ abstract class FileSystemOperationsBased implements CopyActionFacade {
         public WorkResult copy(Action<? super CopySpec> action) {
             return getFileSystemOperations().copy(action);
         }
+
+        @Override
+        public WorkResult delete(Action<? super DeleteSpec> action) {
+            return getFileSystemOperations().delete(action);
+        }
     }
 }
diff --git a/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy b/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
index 2e6f2510..ff419f2e 100644
--- a/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/GenerateProtoTask.groovy
@@ -81,6 +81,7 @@ public abstract class GenerateProtoTask extends DefaultTask {
   static final int CMD_ARGUMENT_EXTRA_LENGTH = 3
   private static final String JAR_SUFFIX = ".jar"
 
+  private final CopyActionFacade copyActionFacade = CopyActionFacade.Loader.create(project, objectFactory)
   // include dirs are passed to the '-I' option of protoc.  They contain protos
   // that may be "imported" from the source protos, but will not be compiled.
   private final ConfigurableFileCollection includeDirs = objectFactory.fileCollection()
@@ -587,6 +588,9 @@ public abstract class GenerateProtoTask extends DefaultTask {
   void compile() {
     Preconditions.checkState(state == State.FINALIZED, 'doneConfig() has not been called')
 
+    copyActionFacade.delete { spec ->
+      spec.delete(outputBaseDir)
+    }
     // Sort to ensure generated descriptors have a canonical representation
     // to avoid triggering unnecessary rebuilds downstream
     List<File> protoFiles = sourceDirs.asFileTree.files.sort()
diff --git a/src/main/groovy/com/google/protobuf/gradle/ProtobufExtension.groovy b/src/main/groovy/com/google/protobuf/gradle/ProtobufExtension.groovy
index 74c090e0..0de530f8 100644
--- a/src/main/groovy/com/google/protobuf/gradle/ProtobufExtension.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/ProtobufExtension.groovy
@@ -37,6 +37,7 @@ import groovy.transform.TypeCheckingMode
 import org.gradle.api.Action
 import org.gradle.api.NamedDomainObjectContainer
 import org.gradle.api.Project
+import org.gradle.api.provider.Property
 import org.gradle.api.tasks.TaskCollection
 
 /**
@@ -52,18 +53,16 @@ abstract class ProtobufExtension {
   private final ArrayList<Action<GenerateProtoTaskCollection>> taskConfigActions
   private final NamedDomainObjectContainer<ProtoSourceSet> sourceSets
 
-  /**
-   * The base directory of generated files. The default is
-   * "${project.buildDir}/generated/source/proto".
-   */
-  private String generatedFilesBaseDir
+  @PackageScope
+  final String defaultGeneratedFilesBaseDir
 
   public ProtobufExtension(final Project project) {
     this.project = project
     this.tasks = new GenerateProtoTaskCollection(project)
     this.tools = new ToolsLocator(project)
     this.taskConfigActions = []
-    this.generatedFilesBaseDir = "${project.buildDir}/generated/source/proto"
+    this.defaultGeneratedFilesBaseDir = "${project.buildDir}/generated/source/proto"
+    this.generatedFilesBaseDirProperty.convention(defaultGeneratedFilesBaseDir)
     this.sourceSets = project.objects.domainObjectContainer(ProtoSourceSet) { String name ->
       new DefaultProtoSourceSet(name, project.objects)
     }
@@ -80,13 +79,21 @@ abstract class ProtobufExtension {
   }
 
   String getGeneratedFilesBaseDir() {
-    return generatedFilesBaseDir
+    return generatedFilesBaseDirProperty.get()
   }
 
+  @Deprecated
   void setGeneratedFilesBaseDir(String generatedFilesBaseDir) {
-    this.generatedFilesBaseDir = generatedFilesBaseDir
+    generatedFilesBaseDirProperty.set(generatedFilesBaseDir)
   }
 
+  /**
+   * The base directory of generated files. The default is
+   * "${project.buildDir}/generated/source/proto".
+   */
+  @PackageScope
+  abstract Property<String> getGeneratedFilesBaseDirProperty()
+
   @PackageScope
   void configureTasks() {
     this.taskConfigActions.each { action ->
diff --git a/src/main/groovy/com/google/protobuf/gradle/ProtobufExtract.groovy b/src/main/groovy/com/google/protobuf/gradle/ProtobufExtract.groovy
index 3da54eab..faafcae8 100644
--- a/src/main/groovy/com/google/protobuf/gradle/ProtobufExtract.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/ProtobufExtract.groovy
@@ -57,7 +57,7 @@ import javax.inject.Inject
 @CompileStatic
 abstract class ProtobufExtract extends DefaultTask {
 
-  private final CopyActionFacade copyActionFacade = instantiateCopyActionFacade()
+  private final CopyActionFacade copyActionFacade = CopyActionFacade.Loader.create(project, objectFactory)
   private final ArchiveActionFacade archiveActionFacade = instantiateArchiveActionFacade()
   private final FileCollection filteredProtos = instantiateFilteredProtos()
 
@@ -98,14 +98,6 @@ abstract class ProtobufExtract extends DefaultTask {
   @Inject
   protected abstract ProviderFactory getProviderFactory()
 
-  private CopyActionFacade instantiateCopyActionFacade() {
-    if (GradleVersion.current() >= GradleVersion.version("6.0")) {
-      // Use object factory to instantiate as that will inject the necessary service.
-      return objectFactory.newInstance(CopyActionFacade.FileSystemOperationsBased)
-    }
-    return new CopyActionFacade.ProjectBased(project)
-  }
-
   private ArchiveActionFacade instantiateArchiveActionFacade() {
     if (GradleVersion.current() >= GradleVersion.version("6.0")) {
       // Use object factory to instantiate as that will inject the necessary service.
diff --git a/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy b/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
index 8d237f4c..9853f0ee 100644
--- a/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
+++ b/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy
@@ -374,15 +374,29 @@ class ProtobufPlugin implements Plugin<Project> {
     ) {
       String sourceSetName = protoSourceSet.name
       String taskName = 'generate' + Utils.getSourceSetSubstringForTaskNames(sourceSetName) + 'Proto'
-      Provider<String> outDir = project.providers.provider {
-        "${this.protobufExtension.generatedFilesBaseDir}/${sourceSetName}".toString()
-      }
+      String defaultGeneratedFilesBaseDir = protobufExtension.defaultGeneratedFilesBaseDir
+      Provider<String> generatedFilesBaseDirProvider = protobufExtension.generatedFilesBaseDirProperty
       Provider<GenerateProtoTask> task = project.tasks.register(taskName, GenerateProtoTask) {
+        CopyActionFacade copyActionFacade = CopyActionFacade.Loader.create(it.project, it.objectFactory)
         it.description = "Compiles Proto source for '${sourceSetName}'".toString()
-        it.outputBaseDir = outDir
+        it.outputBaseDir = project.providers.provider {
+          "${defaultGeneratedFilesBaseDir}/${sourceSetName}".toString()
+        }
         it.addSourceDirs(protoSourceSet.proto)
         it.addIncludeDir(protoSourceSet.proto.sourceDirectories)
         it.addIncludeDir(protoSourceSet.includeProtoDirs)
+        it.doLast { task ->
+          String generatedFilesBaseDir = generatedFilesBaseDirProvider.get()
+          if (generatedFilesBaseDir == defaultGeneratedFilesBaseDir) {
+            return
+          }
+          // Purposefully don't wire this up to outputs, as it can be mixed with other files.
+          copyActionFacade.copy { CopySpec spec ->
+            spec.includeEmptyDirs = false
+            spec.from(it.outputBaseDir)
+            spec.into("${generatedFilesBaseDir}/${sourceSetName}")
+          }
+        }
         configureAction.execute(it)
       }
       protoSourceSet.output.from(task.map { GenerateProtoTask it -> it.outputSourceDirectories })