diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/Kapt3KotlinGradleSubplugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/Kapt3KotlinGradleSubplugin.kt
index 21f71c62a22..4d0544333bb 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/Kapt3KotlinGradleSubplugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/Kapt3KotlinGradleSubplugin.kt
@@ -138,6 +138,7 @@ class Kapt3KotlinGradleSubplugin : KotlinGradleSubplugin<KotlinCompile> {
 
         val kaptClasspath = arrayListOf<File>()
         val buildDependencies = arrayListOf<TaskDependency>()
+        val kaptConfigurations = arrayListOf<Configuration>()
 
         fun handleSourceSet(sourceSetName: String) {
             val kaptConfiguration = project.findKaptConfiguration(sourceSetName)
@@ -146,6 +147,7 @@ class Kapt3KotlinGradleSubplugin : KotlinGradleSubplugin<KotlinCompile> {
             } ?: emptyList()
 
             if (kaptConfiguration != null) {
+                kaptConfigurations += kaptConfiguration
                 buildDependencies += kaptConfiguration.buildDependencies
 
                 if (filteredDependencies.isNotEmpty()) {
@@ -178,6 +180,8 @@ class Kapt3KotlinGradleSubplugin : KotlinGradleSubplugin<KotlinCompile> {
         val kaptGenerateStubsTask = context.createKaptGenerateStubsTask()
         val kaptTask = context.createKaptKotlinTask()
 
+        kaptGenerateStubsTask.source(*kaptConfigurations.toTypedArray())
+
         kaptGenerateStubsTask.dependsOn(*buildDependencies.toTypedArray())
         kaptGenerateStubsTask.dependsOn(*kotlinCompile.dependsOn.toTypedArray())