diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KaptIncrementalIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KaptIncrementalIT.kt
index 9c51178b7e3..9bdd60cca8b 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KaptIncrementalIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KaptIncrementalIT.kt
@@ -1,10 +1,8 @@
 package org.jetbrains.kotlin.gradle
 
-import org.jetbrains.kotlin.gradle.util.allKotlinFiles
-import org.jetbrains.kotlin.gradle.util.findFileByName
-import org.jetbrains.kotlin.gradle.util.getFileByName
-import org.jetbrains.kotlin.gradle.util.modify
+import org.jetbrains.kotlin.gradle.util.*
 import org.junit.Test
+import kotlin.test.assertEquals
 
 open class KaptIncrementalIT : BaseGradleIT() {
     companion object {
@@ -204,6 +202,35 @@ open class KaptIncrementalIT : BaseGradleIT() {
         }
     }
 
+    @Test
+    fun testRemoveAllKotlinSources() {
+        val project = getProject()
+        val kapt3StubsPath = "build/tmp/kapt3/stubs/main"
+
+        project.build("build") {
+            assertSuccessful()
+            assertKapt3FullyExecuted()
+        }
+
+        with(project.projectDir) {
+            resolve("src/main/java").deleteRecursively()
+            resolve("src/main/java/bar").mkdirs()
+            resolve("src/main/java/bar/MyClass.java").writeText(
+                """
+                package bar;
+                public class MyClass {}
+            """.trimIndent()
+            )
+        }
+
+        project.build("build") {
+            assertSuccessful()
+
+            // Make sure all stubs are removed
+            assertEquals(emptyList(), fileInWorkingDir(kapt3StubsPath).walk().filter { it.extension == "java" }.toList())
+        }
+    }
+
     @Test
     fun testRemoveAnnotations() {
         val project = getProject()
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
index 31f76b2236f..0931274bdba 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt
@@ -296,7 +296,8 @@ abstract class AbstractKotlinCompile<T : CommonCompilerArguments>() : AbstractKo
 
         logger.kotlinDebug { "All kotlin sources: ${allKotlinSources.pathsAsStringRelativeTo(project.rootProject.projectDir)}" }
 
-        if (allKotlinSources.isEmpty()) {
+        if (!inputs.isIncremental && allKotlinSources.isEmpty()) {
+            // Skip running only if non-incremental run. Otherwise, we may need to do some cleanup.
             logger.kotlinDebug { "No Kotlin files found, skipping Kotlin compiler task" }
             return
         }