diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
index 045231f49ce..03fdae18bc4 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
@@ -174,7 +174,7 @@ class KlibBasedMppIT : BaseGradleIT() {
 
             assertFileExists("build/classes/kotlin/metadata/commonMain/default/manifest")
             assertFileExists("build/classes/kotlin/metadata/jvmAndJsMain/default/manifest")
-            assertFileExists("build/classes/kotlin/metadata/linuxMain/${projectName}_linuxMain.klib")
+            assertFileExists("build/classes/kotlin/metadata/linuxMain/klib/${projectName}_linuxMain.klib")
 
             // Check that the common and JVM+JS source sets don't receive the Kotlin/Native stdlib in the classpath:
             run {
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 072ee4dbff2..e1859e360ea 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
@@ -1628,7 +1628,7 @@ class NewMultiplatformIT : BaseGradleIT() {
                 )
 
                 // Native:
-                assertFileExists("build/classes/kotlin/linux64/integrationTest/new-mpp-associate-compilations_integrationTest.klib")
+                assertFileExists("build/classes/kotlin/linux64/integrationTest/klib/new-mpp-associate-compilations_integrationTest.klib")
             }
 
             gradleBuildScript().appendText(
@@ -1706,10 +1706,10 @@ class NewMultiplatformIT : BaseGradleIT() {
                     }
                 }
 
-            val interopManifest = getManifest("foo/build/classes/kotlin/linux/main/foo-cinterop-bar.klib")
+            val interopManifest = getManifest("foo/build/classes/kotlin/linux/main/cinterop/foo-cinterop-bar.klib")
             assertEquals("org.sample.one:foo-cinterop-bar", interopManifest[KLIB_PROPERTY_UNIQUE_NAME])
 
-            val nativeManifest = getManifest("foo/build/classes/kotlin/linux/main/foo.klib")
+            val nativeManifest = getManifest("foo/build/classes/kotlin/linux/main/klib/foo.klib")
             assertEquals("org.sample.one:foo", nativeManifest[KLIB_PROPERTY_UNIQUE_NAME])
             // Check the short name that is used as a prefix in generated ObjC headers.
             assertEquals("foo", nativeManifest[KLIB_PROPERTY_SHORT_NAME])
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/native/GeneralNativeIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/native/GeneralNativeIT.kt
index dba667e5a00..cc93c42610a 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/native/GeneralNativeIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/native/GeneralNativeIT.kt
@@ -166,7 +166,7 @@ class GeneralNativeIT : BaseGradleIT() {
 
         val klibPrefix = CompilerOutputKind.LIBRARY.prefix(HostManager.host)
         val klibSuffix = CompilerOutputKind.LIBRARY.suffix(HostManager.host)
-        val klibPath = "${targetClassesDir("host")}${klibPrefix}native-library$klibSuffix"
+        val klibPath = "${targetClassesDir("host")}${klibPrefix}/klib/native-library$klibSuffix"
 
         val linkTasks = listOf(
             ":linkDebugSharedHost",
@@ -772,9 +772,9 @@ class GeneralNativeIT : BaseGradleIT() {
     @Test
     fun testCinterop() = with(transformNativeTestProjectWithPluginDsl("native-cinterop")) {
         fun libraryFiles(projectName: String, cinteropName: String) = listOf(
-            "$projectName/build/classes/kotlin/host/main/${projectName}-cinterop-$cinteropName.klib",
-            "$projectName/build/classes/kotlin/host/main/${projectName}.klib",
-            "$projectName/build/classes/kotlin/host/test/${projectName}_test.klib",
+            "$projectName/build/classes/kotlin/host/main/cinterop/${projectName}-cinterop-$cinteropName.klib",
+            "$projectName/build/classes/kotlin/host/main/klib/${projectName}.klib",
+            "$projectName/build/classes/kotlin/host/test/klib/${projectName}_test.klib",
         )
 
         // Enable info log to see cinterop environment variables.
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/common-klib-lib-and-app/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/common-klib-lib-and-app/build.gradle.kts
index 6889b1f6015..5a358107ac5 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/common-klib-lib-and-app/build.gradle.kts
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/common-klib-lib-and-app/build.gradle.kts
@@ -94,7 +94,7 @@ tasks {
 		if (target in skipCompilationOfTargets) {
 			actions.clear()
 			doLast { 
-				val destinationFile = project.buildDir.resolve("classes/kotlin/$target/main/${project.name}.klib")
+				val destinationFile = project.buildDir.resolve("classes/kotlin/$target/main/klib/${project.name}.klib")
 				destinationFile.parentFile.mkdirs()
 				println("Writing a dummy klib to $destinationFile")
 				destinationFile.createNewFile()
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetConfigurator.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetConfigurator.kt
index c14063e42ef..9c4941cb0bc 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetConfigurator.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetConfigurator.kt
@@ -260,7 +260,7 @@ open class KotlinNativeTargetConfigurator<T : KotlinNativeTarget>(
                     "compilation for target '${compilation.platformType.name}'."
             it.enabled = compilation.konanTarget.enabledOnCurrentHost
 
-            it.destinationDir = klibOutputDirectory(compilation)
+            it.destinationDir = klibOutputDirectory(compilation).resolve("klib")
         }
 
 
@@ -292,7 +292,7 @@ open class KotlinNativeTargetConfigurator<T : KotlinNativeTarget>(
         compilation.cinterops.all { interop ->
             val interopTask = registerTask<CInteropProcess>(interop.interopProcessingTaskName) {
                 it.settings = interop
-                it.destinationDir = provider { klibOutputDirectory(compilation) }
+                it.destinationDir = provider { klibOutputDirectory(compilation).resolve("cinterop") }
                 it.group = INTEROP_GROUP
                 it.description = "Generates Kotlin/Native interop library '${interop.name}' " +
                         "for compilation '${compilation.name}'" +