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 062213d886a..ea2093fd1d9 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
@@ -934,20 +934,20 @@ class NewMultiplatformIT : BaseGradleIT() {
     @Test
     fun testNativeBinaryGroovyDSL() = doTestNativeBinaryDSL("groovy-dsl")
 
+    private fun CompiledProject.checkNativeCommandLineFor(vararg taskPaths: String, check: (String) -> Unit) = taskPaths.forEach { taskPath ->
+        val commandLine = output.lineSequence().dropWhile {
+            !it.contains("Executing actions for task '$taskPath'")
+        }.first {
+            it.contains("Run tool: konanc")
+        }
+        check(commandLine)
+    }
+
     private fun doTestNativeBinaryDSL(
         projectName: String,
         gradleVersionRequired: GradleVersionRequired = gradleVersion
     ) = with(transformProjectWithPluginsDsl(projectName, gradleVersionRequired, "new-mpp-native-binaries")) {
 
-        fun CompiledProject.checkCommandLineFor(vararg taskPaths: String, check: (String) -> Unit) = taskPaths.forEach { taskPath ->
-            val commandLine = output.lineSequence().dropWhile {
-                !it.contains("Executing actions for task '$taskPath'")
-            }.first {
-                it.contains("Run tool: konanc")
-            }
-            check(commandLine)
-        }
-
         val hostSuffix = nativeHostTargetName.capitalize()
         val binaries = mutableListOf(
             "debugExecutable" to "native-binary",
@@ -1013,7 +1013,7 @@ class NewMultiplatformIT : BaseGradleIT() {
         // Check that kotlinOptions work fine for a compilation.
         build(compileTask) {
             assertSuccessful()
-            checkCommandLineFor(":$compileTask") {
+            checkNativeCommandLineFor(":$compileTask") {
                 assertTrue(it.contains("-verbose"))
             }
         }
@@ -1032,7 +1032,7 @@ class NewMultiplatformIT : BaseGradleIT() {
         build("runTest2ReleaseExecutable$hostSuffix") {
             assertSuccessful()
             assertTasksExecuted(":$compileTestTask")
-            checkCommandLineFor(":linkTest2ReleaseExecutable$hostSuffix") {
+            checkNativeCommandLineFor(":linkTest2ReleaseExecutable$hostSuffix") {
                 assertTrue(it.contains("-tr"))
                 assertTrue(it.contains("-Xtime"))
                 // Check that kotlinOptions of the compilation don't affect the binary.
@@ -1057,7 +1057,7 @@ class NewMultiplatformIT : BaseGradleIT() {
                 fileInWorkingDir("build/bin/ios/releaseFramework/native_binary.framework/Headers/native_binary.h")
                     .readText().contains("+ (int32_t)exported")
                 // Check that by default release frameworks have bitcode embedded.
-                checkCommandLineFor(":linkReleaseFrameworkIos") {
+                checkNativeCommandLineFor(":linkReleaseFrameworkIos") {
                     assertTrue(it.contains("-Xembed-bitcode"))
                     assertTrue(it.contains("-opt"))
                 }
@@ -1070,7 +1070,7 @@ class NewMultiplatformIT : BaseGradleIT() {
                 fileInWorkingDir("build/bin/ios/debugFramework/native_binary.framework/Headers/native_binary.h")
                     .readText().contains("+ (int32_t)exported")
                 // Check that by default debug frameworks have bitcode marker embedded.
-                checkCommandLineFor(":linkDebugFrameworkIos") {
+                checkNativeCommandLineFor(":linkDebugFrameworkIos") {
                     assertTrue(it.contains("-Xembed-bitcode-marker"))
                     assertTrue(it.contains("-g"))
                 }
@@ -1079,7 +1079,7 @@ class NewMultiplatformIT : BaseGradleIT() {
             // Check manual disabling bitcode embedding, custom command line args and building a static framework.
             build("linkCustomReleaseFrameworkIos") {
                 assertSuccessful()
-                checkCommandLineFor(":linkCustomReleaseFrameworkIos") {
+                checkNativeCommandLineFor(":linkCustomReleaseFrameworkIos") {
                     assertTrue(it.contains("-linker-option -L."))
                     assertTrue(it.contains("-Xtime"))
                     assertTrue(it.contains("-Xstatic-framework"))
@@ -1093,7 +1093,7 @@ class NewMultiplatformIT : BaseGradleIT() {
                 assertSuccessful()
                 assertFileExists("build/bin/iosSim/releaseFramework/native_binary.framework")
                 assertFileExists("build/bin/iosSim/debugFramework/native_binary.framework")
-                checkCommandLineFor(":linkReleaseFrameworkIosSim", ":linkDebugFrameworkIosSim") {
+                checkNativeCommandLineFor(":linkReleaseFrameworkIosSim", ":linkDebugFrameworkIosSim") {
                     assertFalse(it.contains("-Xembed-bitcode"))
                     assertFalse(it.contains("-Xembed-bitcode-marker"))
                 }
@@ -1117,6 +1117,30 @@ class NewMultiplatformIT : BaseGradleIT() {
         }
     }
 
+    // Check that we still can build binaries from sources if the corresponding property is specified.
+    // TODO: Drop in 1.3.70.
+    @Test
+    fun testLinkNativeBinaryFromSources() = with(
+        transformProjectWithPluginsDsl("groovy-dsl", gradleVersion, "new-mpp-native-binaries")
+    ) {
+        val linkTask = ":linkDebugExecutable${nativeHostTargetName.capitalize()}"
+
+        val prefix = CompilerOutputKind.PROGRAM.prefix(HostManager.host)
+        val suffix = CompilerOutputKind.PROGRAM.suffix(HostManager.host)
+        val fileName = "${prefix}native-binary$suffix"
+        val outputFile = "build/bin/$nativeHostTargetName/debugExecutable/$fileName"
+
+        build(linkTask, "-Pkotlin.native.linkFromSources") {
+            assertSuccessful()
+            assertTasksExecuted(linkTask)
+            assertFileExists(outputFile)
+            checkNativeCommandLineFor(linkTask) {
+                assertTrue(it.contains("-Xcommon-sources="))
+                assertTrue(it.contains(projectDir.resolve("src/commonMain/kotlin/RootMain.kt").absolutePath))
+            }
+        }
+    }
+
     @Test
     fun testNativeFreeArgsWarning() = with(transformProjectWithPluginsDsl("kotlin-dsl", gradleVersion, "new-mpp-native-binaries")) {
         gradleBuildScript().appendText(
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/tasks/KotlinNativeTasks.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/tasks/KotlinNativeTasks.kt
index 1a0d02ee0ee..9c193a6a2ec 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/tasks/KotlinNativeTasks.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/tasks/KotlinNativeTasks.kt
@@ -360,7 +360,9 @@ open class KotlinNativeCompile : AbstractKotlinNativeCompile<KotlinCommonOptions
 open class KotlinNativeLink : AbstractKotlinNativeCompile<KotlinCommonToolOptions>() {
 
     init {
-        dependsOn(project.provider { compilation.compileKotlinTask })
+        if (!linkFromSources) {
+            dependsOn(project.provider { compilation.compileKotlinTask })
+        }
     }
 
     @Internal
@@ -370,12 +372,21 @@ open class KotlinNativeLink : AbstractKotlinNativeCompile<KotlinCommonToolOption
     override val compilation: KotlinNativeCompilation
         get() = binary.compilation
 
-    @InputFile
+    @Internal // Taken into account by getSources().
     val intermediateLibrary: Provider<File> = project.provider {
         compilation.compileKotlinTask.outputFile.get()
     }
 
-    override fun getSource(): FileTree = project.files(intermediateLibrary.get()).asFileTree
+    @InputFiles
+    @SkipWhenEmpty
+    override fun getSource(): FileTree =
+        if (linkFromSources) {
+            // Allow a user to force the old behaviour of a link task.
+            // TODO: Remove in 1.3.70.
+            project.files(compilation.allSources).asFileTree
+        } else {
+            project.files(intermediateLibrary.get()).asFileTree
+        }
 
     @get:Input
     override val outputKind: CompilerOutputKind
@@ -443,6 +454,13 @@ open class KotlinNativeLink : AbstractKotlinNativeCompile<KotlinCommonToolOption
     val embedBitcode: Framework.BitcodeEmbeddingMode
         get() = (binary as? Framework)?.embedBitcode ?: Framework.BitcodeEmbeddingMode.DISABLE
 
+    // This property allows a user to force the old behaviour of a link task
+    // to workaround issues that may occur after switching to the two-stage linking.
+    // If it is specified, the final binary is built directly from sources instead of a klib.
+    // TODO: Remove it in 1.3.70.
+    private val linkFromSources: Boolean
+        get() = project.hasProperty(LINK_FROM_SOURCES_PROPERTY)
+
     override fun buildCompilerArgs(): List<String> = mutableListOf<String>().apply {
         addAll(super.buildCompilerArgs())
 
@@ -462,7 +480,25 @@ open class KotlinNativeLink : AbstractKotlinNativeCompile<KotlinCommonToolOption
         addKey("-Xstatic-framework", isStaticFramework)
     }
 
-    override fun buildSourceArgs(): List<String> = listOf("-Xinclude=${intermediateLibrary.get().absolutePath}")
+    override fun buildSourceArgs(): List<String> {
+        return if (!linkFromSources) {
+            listOf("-Xinclude=${intermediateLibrary.get().absolutePath}")
+        } else {
+            // Allow a user to force the old behaviour of a link task.
+            // TODO: Remove in 1.3.70.
+            mutableListOf<String>().apply {
+                val friends = compilation.friendCompilation?.output?.allOutputs?.files
+                if (friends != null && friends.isNotEmpty()) {
+                    addArg("-friend-modules", friends.joinToString(File.pathSeparator) { it.absolutePath })
+                }
+
+                addAll(project.files(compilation.allSources).map { it.absolutePath })
+                if (!compilation.commonSources.isEmpty) {
+                    add("-Xcommon-sources=${compilation.commonSources.joinToString(separator = ",") { it.absolutePath }}")
+                }
+            }
+        }
+    }
 
     private fun validatedExportedLibraries() {
         val exportConfiguration = exportLibraries as? Configuration ?: return
@@ -500,6 +536,10 @@ open class KotlinNativeLink : AbstractKotlinNativeCompile<KotlinCommonToolOption
         validatedExportedLibraries()
         super.compile()
     }
+
+    companion object {
+        private const val LINK_FROM_SOURCES_PROPERTY = "kotlin.native.linkFromSources"
+    }
 }
 
 open class CInteropProcess : DefaultTask() {