diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/metadata/K2MetadataKlibSerializer.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/metadata/K2MetadataKlibSerializer.kt
index d185b7f87c8..1a7791c08b6 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/metadata/K2MetadataKlibSerializer.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/metadata/K2MetadataKlibSerializer.kt
@@ -52,7 +52,7 @@ internal class K2MetadataKlibSerializer(private val metadataVersion: BuiltInsBin
             LockBasedStorageManager("K2MetadataKlibSerializer")
         )
 
-        val analyzer = runCommonAnalysisForSerialization(environment, false, dependencyContainer)
+        val analyzer = runCommonAnalysisForSerialization(environment, true, dependencyContainer)
 
         if (analyzer == null || analyzer.hasErrors()) return
 
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 61eaf856984..c1185726b61 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
@@ -8,8 +8,9 @@ package org.jetbrains.kotlin.gradle
 import org.jetbrains.kotlin.gradle.util.modify
 import org.jetbrains.kotlin.konan.target.HostManager
 import org.junit.Assume
-import kotlin.test.Ignore
+import java.io.File
 import kotlin.test.Test
+import kotlin.test.assertFalse
 
 /** FIXME (sergey.igushkin): please enable these tests back as soon as the Kotlin/Native version that is bundled with the
  *        Kotlin distribution supports compilation to klib and targetless klibs.
@@ -89,6 +90,23 @@ class KlibBasedMppIT : BaseGradleIT() {
             assertSuccessful()
 
             assertTasksExecuted(*tasksToExecute.toTypedArray())
+
+            assertFileExists("build/classes/kotlin/metadata/jvmAndJsMain/manifest")
+            assertFileExists("build/classes/kotlin/metadata/iosMain/iosMain.klib")
+
+            // Check that the common and JVM+JS source sets don't receive the Kotlin/Native stdlib in the classpath:
+            run {
+                fun getClasspath(taskPath: String): Iterable<String> {
+                    val argsPrefix = " $taskPath Kotlin compiler args:"
+                    return output.lines().single { argsPrefix in it }
+                        .substringAfter("-classpath ").substringBefore(" -").split(File.pathSeparator)
+                }
+
+                fun classpathHasKNStdlib(classpath: Iterable<String>) = classpath.any { "klib/common/stdlib" in it.replace("\\", "/") }
+
+                assertFalse(classpathHasKNStdlib(getClasspath(":compileKotlinMetadata")))
+                assertFalse(classpathHasKNStdlib(getClasspath(":compileJvmAndJsMainKotlinMetadata")))
+            }
         }
     }
 }
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/GradleKotlinCompilerWork.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/GradleKotlinCompilerWork.kt
index 4ebf85b37cd..0395a092896 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/GradleKotlinCompilerWork.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/GradleKotlinCompilerWork.kt
@@ -126,7 +126,7 @@ internal class GradleKotlinCompilerWork @Inject constructor(
         with(log) {
             kotlinDebug { "Kotlin compiler class: ${compilerClassName}" }
             kotlinDebug { "Kotlin compiler classpath: ${compilerFullClasspath.joinToString { it.canonicalPath }}" }
-            kotlinDebug { "Kotlin compiler args: ${compilerArgs.joinToString(" ")}" }
+            kotlinDebug { "$taskPath Kotlin compiler args: ${compilerArgs.joinToString(" ")}" }
         }
 
         val executionStrategy = kotlinCompilerExecutionStrategy()
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetPreset.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetPreset.kt
index ef358813e13..b54d93ecb79 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetPreset.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/KotlinNativeTargetPreset.kt
@@ -142,7 +142,7 @@ abstract class AbstractKotlinNativeTargetPreset<T : KotlinNativeTarget>(
             project.kotlinExtension.sourceSets
                 .filter { it.isIntermediateNativeSourceSet() }
                 .forEach {
-                    it.dependencies { implementation(stdlib) }
+                    project.dependencies.add(it.implementationMetadataConfigurationName, stdlib)
                 }
         }
     }