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 44243efe399..b8251d5529b 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
@@ -242,6 +242,57 @@ class CommonizerIT : BaseGradleIT() {
         }
     }
 
+    @Test
+    fun `test KT-46234 intermediate source set with only one native target`() {
+
+        val posixInImplementationMetadataConfigurationRegex = Regex(""".*implementationMetadataConfiguration:.*([pP])osix""")
+        val posixInIntransitiveMetadataConfigurationRegex = Regex(""".*intransitiveMetadataConfiguration:.*([pP])osix""")
+
+        fun CompiledProject.containsPosixInImplementationMetadataConfiguration(): Boolean =
+            output.lineSequence().any { line ->
+                line.matches(posixInImplementationMetadataConfigurationRegex)
+            }
+
+        fun CompiledProject.containsPosixInIntransitiveMetadataConfiguration(): Boolean =
+            output.lineSequence().any { line ->
+                line.matches(posixInIntransitiveMetadataConfigurationRegex)
+            }
+
+        with(Project("commonize-kt-46234-singleNativeTarget")) {
+            build(":p1:listNativePlatformMainDependencies", "-Pkotlin.mpp.enableIntransitiveMetadataConfiguration=false") {
+                assertSuccessful()
+
+                assertTrue(
+                    containsPosixInImplementationMetadataConfiguration(),
+                    "Expected dependency on posix in implementationMetadataConfiguration"
+                )
+
+                assertFalse(
+                    containsPosixInIntransitiveMetadataConfiguration(),
+                    "Expected **no** dependency on posix in intransitiveMetadataConfiguration"
+                )
+            }
+
+            build(":p1:listNativePlatformMainDependencies", "-Pkotlin.mpp.enableIntransitiveMetadataConfiguration=true") {
+                assertSuccessful()
+
+                assertFalse(
+                    containsPosixInImplementationMetadataConfiguration(),
+                    "Expected **no** posix dependency in implementationMetadataConfiguration"
+                )
+
+                assertTrue(
+                    containsPosixInIntransitiveMetadataConfiguration(),
+                    "Expected dependency on posix in intransitiveMetadataConfiguration"
+                )
+            }
+
+            build("assemble") {
+                assertSuccessful()
+            }
+        }
+    }
+
     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-46234-singleNativeTarget/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/build.gradle.kts
new file mode 100644
index 00000000000..448f4930cb0
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/build.gradle.kts
@@ -0,0 +1,10 @@
+plugins {
+    kotlin("multiplatform") apply false
+}
+
+allprojects {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/gradle.properties b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/gradle.properties
new file mode 100644
index 00000000000..1d227bf1304
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/gradle.properties
@@ -0,0 +1,3 @@
+kotlin.mpp.enableGranularSourceSetsMetadata=true
+kotlin.native.enableDependencyPropagation=false
+kotlin.mpp.enableIntransitiveMetadataConfiguration=true
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/build.gradle.kts
new file mode 100644
index 00000000000..10b31f4de6e
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/build.gradle.kts
@@ -0,0 +1,61 @@
+import org.jetbrains.kotlin.com.intellij.openapi.util.SystemInfo.*
+import org.jetbrains.kotlin.gradle.plugin.KotlinSourceSet
+
+operator fun KotlinSourceSet.invoke(builder: SourceSetHierarchyBuilder.() -> Unit): KotlinSourceSet {
+    SourceSetHierarchyBuilder(this).builder()
+    return this
+}
+
+class SourceSetHierarchyBuilder(private val node: KotlinSourceSet) {
+    operator fun KotlinSourceSet.unaryMinus() = this.dependsOn(node)
+}
+
+plugins {
+    kotlin("multiplatform")
+}
+
+kotlin {
+
+    val nativePlatform = when {
+        isMac -> macosX64("nativePlatform")
+        isLinux -> linuxX64("nativePlatform")
+        isWindows -> mingwX64("nativePlatform")
+        else -> throw IllegalStateException("Unsupported host")
+    }
+
+    val commonMain by sourceSets.getting
+    val nativeMain by sourceSets.creating
+    val nativePlatformMain by sourceSets.getting
+
+    commonMain {
+        -nativeMain {
+            -nativePlatformMain
+        }
+    }
+
+    tasks.register("listNativePlatformMainDependencies") {
+        doLast {
+
+            val implementationMetadataConfigurationDependencies = project.configurations.getByName(
+                nativePlatformMain.implementationMetadataConfigurationName
+            ).files
+
+            val intransitiveMetadataConfigurationDependencies = project.configurations.findByName(
+                "nativePlatformMainIntransitiveDependenciesMetadata"
+            )?.files.orEmpty()
+
+            val dependencies = implementationMetadataConfigurationDependencies +
+                    intransitiveMetadataConfigurationDependencies
+
+            logger.quiet("NativePlatformMainDependency | Count: ${dependencies.size}")
+
+            implementationMetadataConfigurationDependencies.forEach { dependencyFile ->
+                logger.quiet("implementationMetadataConfiguration: ${dependencyFile.path}")
+            }
+
+            intransitiveMetadataConfigurationDependencies.forEach { dependencyFile ->
+                logger.quiet("intransitiveMetadataConfiguration: ${dependencyFile.path}")
+            }
+        }
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/src/nativePlatformMain/kotlin/NativePlatformMain.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/src/nativePlatformMain/kotlin/NativePlatformMain.kt
new file mode 100644
index 00000000000..66907b37b4f
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/p1/src/nativePlatformMain/kotlin/NativePlatformMain.kt
@@ -0,0 +1,7 @@
+@file:Suppress("unused")
+
+import platform.posix.usleep
+
+fun main() {
+    usleep(100)
+}
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/settings.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/settings.gradle.kts
new file mode 100644
index 00000000000..ac06873d297
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/commonize-kt-46234-singleNativeTarget/settings.gradle.kts
@@ -0,0 +1,12 @@
+pluginManagement {
+    repositories {
+        mavenLocal()
+        gradlePluginPortal()
+    }
+    val kotlin_version: String by settings
+    plugins {
+        kotlin("multiplatform").version(kotlin_version)
+    }
+}
+
+include(":p1")
\ No newline at end of file