diff --git a/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KonanPlugin.kt b/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KonanPlugin.kt
index 1ac77dce1f5..e1e540286eb 100644
--- a/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KonanPlugin.kt
+++ b/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KonanPlugin.kt
@@ -225,6 +225,10 @@ class KonanPlugin @Inject constructor(private val registry: ToolingModelBuilderR
         findByPath(name) ?: create(name, DefaultTask::class.java)
     }
 
+    private fun Project.cleanKonan() = project.konanArtifactsContainer.forEach {
+        project.delete(it.compilationTask.outputDir)
+    }
+
     override fun apply(project: Project?) {
         if (project == null) { return }
         registry.register(KonanToolingModelBuilder)
@@ -254,6 +258,9 @@ class KonanPlugin @Inject constructor(private val registry: ToolingModelBuilderR
         project.getTask("build").apply {
             dependsOn(compileKonanTask)
         }
+        project.getTask("clean").apply {
+            doLast { project.cleanKonan() }
+        }
 
         // Create task to run supported executables.
         project.getOrCreateTask("run").apply {
diff --git a/tools/kotlin-native-gradle-plugin/src/test/groovy/org/jetbrains/kotlin/gradle/plugin/test/PathSpecification.groovy b/tools/kotlin-native-gradle-plugin/src/test/groovy/org/jetbrains/kotlin/gradle/plugin/test/PathSpecification.groovy
index 2a501b85be1..cc16b70dd5c 100644
--- a/tools/kotlin-native-gradle-plugin/src/test/groovy/org/jetbrains/kotlin/gradle/plugin/test/PathSpecification.groovy
+++ b/tools/kotlin-native-gradle-plugin/src/test/groovy/org/jetbrains/kotlin/gradle/plugin/test/PathSpecification.groovy
@@ -38,4 +38,21 @@ class PathSpecification extends BaseKonanSpecification {
         result.task(project.defaultInteropProcessingTask()).outcome == TaskOutcome.FAILED
     }
 
+    def 'Plugin should remove custom output directories'() {
+        when:
+        def customOutputDir = projectDirectory.toPath().resolve("foo").toFile()
+        def project = KonanInteropProject.create(projectDirectory) { KonanProject it ->
+            it.addCompilationSetting("outputDir", customOutputDir)
+        }
+        def res1 = project.createRunner().withArguments("build").build()
+        def customDirExistsAfterBuild = customOutputDir.exists()
+        def res2 = project.createRunner().withArguments("clean").build()
+        def customDirDoesntNotExistAfterClean = !customOutputDir.exists()
+
+        then:
+        res1.taskPaths(TaskOutcome.SUCCESS).containsAll(project.buildingTasks)
+        res2.taskPaths(TaskOutcome.SUCCESS).contains(":clean")
+        customDirExistsAfterBuild
+        customDirDoesntNotExistAfterClean
+    }
 }