diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/CommonizerIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/CommonizerIT.kt
index 8d9383a1169..32c73ea6f73 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/CommonizerIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/CommonizerIT.kt
@@ -675,7 +675,8 @@ class CommonizerIT : BaseGradleIT() {
     fun `test KT-52243 cinterop caching`() {
         with(preparedProject("commonizeCurlInterop")) {
             val localBuildCacheDir = projectDir.resolve("local-build-cache-dir").also { assertTrue(it.mkdirs()) }
-            gradleSettingsScript().appendText("""
+            gradleSettingsScript().appendText(
+                """
                 
                 buildCache {
                     local {
@@ -708,6 +709,20 @@ class CommonizerIT : BaseGradleIT() {
         }
     }
 
+    @Test
+    fun `test KT-56729 commonization with library containing two roots`() {
+        with(Project("commonize-kt-56729-consume-library-with-two-roots")) {
+            build("publish") {
+                assertSuccessful()
+            }
+
+            build(":consumer:assemble") {
+                assertSuccessful()
+                assertTasksExecuted(":consumer:compileCommonMainKotlinMetadata")
+            }
+        }
+    }
+
     private fun preparedProject(name: String): Project {
         return Project(name).apply {
             setupWorkingDir()
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/build.gradle.kts
new file mode 100644
index 00000000000..8d678cbdc60
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/build.gradle.kts
@@ -0,0 +1,30 @@
+@file:Suppress("OPT_IN_USAGE")
+
+import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinNativeTarget
+
+plugins {
+    kotlin("multiplatform")
+}
+
+repositories {
+    maven(project(":producer").buildDir.resolve("repo"))
+    mavenLocal()
+    mavenCentral()
+}
+
+kotlin {
+    linuxArm64()
+    linuxX64()
+
+    targetHierarchy.default()
+
+    sourceSets.commonMain.get().dependencies {
+        implementation("org.jetbrains.sample:producer:1.0.0-SNAPSHOT")
+    }
+
+    targets.withType<KotlinNativeTarget>().all {
+        compilations.getByName("main").cinterops.create("consumer-c-library") {
+            header("src/consumer-c-library.h")
+        }
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/commonMain/kotlin/CommonMain.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/commonMain/kotlin/CommonMain.kt
new file mode 100644
index 00000000000..3c8bfd9f905
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/commonMain/kotlin/CommonMain.kt
@@ -0,0 +1,5 @@
+object CommonMain {
+    init {
+        ProducerNativeCommonMain.fromCInterop().value
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/consumer-c-library.h b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/consumer-c-library.h
new file mode 100644
index 00000000000..657a86e5740
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/consumer-c-library.h
@@ -0,0 +1 @@
+void myConsumerCLibraryFunction();
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/nativeInterop/cinterop/consumer-c-library.def b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/consumer/src/nativeInterop/cinterop/consumer-c-library.def
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/gradle.properties b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/gradle.properties
new file mode 100644
index 00000000000..2db016ae4e4
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/gradle.properties
@@ -0,0 +1 @@
+kotlin.mpp.enableCInteropCommonization=true
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/build.gradle.kts
new file mode 100644
index 00000000000..6c3e7ade3c6
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/build.gradle.kts
@@ -0,0 +1,34 @@
+@file:Suppress("OPT_IN_USAGE")
+
+import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinNativeTarget
+
+plugins {
+    kotlin("multiplatform")
+    `maven-publish`
+}
+
+version = "1.0.0-SNAPSHOT"
+group = "org.jetbrains.sample"
+
+publishing {
+    repositories {
+        maven(buildDir.resolve("repo"))
+    }
+}
+
+kotlin {
+    linuxX64()
+    linuxArm64()
+
+    targetHierarchy.custom {
+        group("nativeCommon") {
+            withNative()
+        }
+    }
+
+    targets.withType<KotlinNativeTarget>().all {
+        compilations.getByName("main").cinterops.create("producer-cinterop-library") {
+            header("src/producer-c-library.h")
+        }
+    }
+}
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/nativeCommonMain/kotlin/ProducerNativeCommonMain.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/nativeCommonMain/kotlin/ProducerNativeCommonMain.kt
new file mode 100644
index 00000000000..a48828cc866
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/nativeCommonMain/kotlin/ProducerNativeCommonMain.kt
@@ -0,0 +1,5 @@
+import `producer-cinterop-library`.ProducerCLibraryStruct
+
+object ProducerNativeCommonMain {
+    fun fromCInterop(): ProducerCLibraryStruct = error("Stub!")
+}
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/nativeInterop/cinterop/producer-cinterop-library.def b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/nativeInterop/cinterop/producer-cinterop-library.def
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/producer-c-library.h b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/producer-c-library.h
new file mode 100644
index 00000000000..3d6d3b1c032
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/producer/src/producer-c-library.h
@@ -0,0 +1,3 @@
+struct ProducerCLibraryStruct {
+    int value;
+};
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/settings.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/settings.gradle.kts
new file mode 100644
index 00000000000..d19eb2d2e8f
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-56729-consume-library-with-two-roots/settings.gradle.kts
@@ -0,0 +1,9 @@
+dependencyResolutionManagement {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+}
+
+include(":producer")
+include(":consumer")