diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
index 23eb74e6430..f042e8b10b7 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt
@@ -292,4 +292,38 @@ class NewMultiplatformIT : BaseGradleIT() {
             assertSuccessful()
         }
     }
+
+    @Test
+    fun testResourceFilteringAndSourceTrackingWithJava() = with(Project("simpleProject")) {
+        setupWorkingDir()
+        gradleBuildScript().appendText(
+            "\n" + """
+            // Test 1 -- check that Kotlin sources are correctly filtered out of resources, even those added late at configuration time:
+            sourceSets.main.resources.srcDir('src/main/kotlin')
+            sourceSets.main.resources.srcDir('src/foo/kotlin')
+            kotlin.target.compilations.main.source(kotlin.sourceSets.create('foo'))
+
+            // Test 2 -- check that Java sources from the Kotlin source directories are correctly tracked under `allJava` in the source set:
+            sourceSets.main.allJava.files.each { println "allJava:${'$'}{it.name}" }
+            """.trimIndent()
+        )
+        listOf("src/foo/kotlin/foo.kt", "src/main/resources/foo.txt", "src/foo/kotlin/foo.java").forEach { path ->
+            projectDir.resolve(path).apply { parentFile.mkdirs(); writeText("foo") }
+        }
+
+        build("processResources") {
+            assertSuccessful()
+
+            // Test 1 (see above)
+            assertTasksExecuted(":processResources")
+            assertFileExists("build/resources/main/foo.txt")
+            assertNoSuchFile("build/resources/main/helloWorld.kt")
+            assertNoSuchFile("build/resources/main/foo.kt")
+
+            // Test 2 (see above)
+            assertContains("allJava:Greeter.java")
+            assertContains("allJava:HelloWorld.java")
+            assertContains("allJava:foo.java")
+        }
+    }
 }
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
index 4602395a8d3..82038462375 100755
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
@@ -37,7 +37,6 @@ import org.jetbrains.kotlin.gradle.tasks.*
 import org.jetbrains.kotlin.gradle.utils.*
 import java.io.File
 import java.net.URL
-import java.util.*
 import java.util.concurrent.Callable
 import java.util.jar.Manifest
 
@@ -116,15 +115,20 @@ internal abstract class KotlinJavaSourceSetProcessor<T : AbstractKotlinCompile<*
         if (javaSourceSet == null)
             return
 
-        val kotlinDirSets = kotlinCompilation.kotlinSourceSets.map(KotlinSourceSet::kotlin)
+        val kotlinDirSets = kotlinCompilation.kotlinSourceSets
 
-        // Try to avoid duplicate Java sources in allSource:
-        val kotlinSrcDirsToAdd = kotlinDirSets.map { filterOutJavaSrcDirsIfPossible(it) }
+        // run lazily to support changing kotlinSourceSets after plugin is applied
+        val kotlinSrcDirsToAdd = Callable {
+            // Try to avoid duplicate Java sources in allSource:
+            kotlinDirSets.map { filterOutJavaSrcDirsIfPossible(it.kotlin) }
+        }
 
-        kotlinSrcDirsToAdd.forEach { kotlinSrcDirs ->
-            javaSourceSet.allJava.srcDirs(kotlinSrcDirs)
-            javaSourceSet.allSource.srcDirs(kotlinSrcDirs)
-            javaSourceSet.resources.filter.exclude { it.file in kotlinSrcDirs }
+        javaSourceSet.allJava.srcDirs(kotlinSrcDirsToAdd)
+        javaSourceSet.allSource.srcDirs(kotlinSrcDirsToAdd)
+
+        javaSourceSet.resources.filter.exclude { fileTreeElement ->
+            val file = fileTreeElement.file
+            kotlinDirSets.any { file in it.kotlin }
         }
     }