diff --git a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/SourceSetCommonizerTargetTest.kt b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/SourceSetCommonizerTargetTest.kt
index 723f6df8a31..8b60c05f472 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/SourceSetCommonizerTargetTest.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/SourceSetCommonizerTargetTest.kt
@@ -177,4 +177,32 @@ class SourceSetCommonizerTargetTest {
 
         assertNull(project.getCommonizerTarget(nativeMain), "Expected no commonizer target, since no real source set hierarchy is given")
     }
+
+    @Test
+    fun `orphan source sets are ignored`() {
+        val linux1 = kotlin.linuxX64("linux1")
+        val linux2 = kotlin.linuxArm64("linux2")
+        val nativeMain = kotlin.sourceSets.create("nativeMain")
+        val linux1Main = kotlin.sourceSets.getByName("linux1Main")
+        val linux2Main = kotlin.sourceSets.getByName("linux2Main")
+        val orphan = kotlin.sourceSets.create("orphan")
+
+        linux1Main.dependsOn(nativeMain)
+        linux2Main.dependsOn(nativeMain)
+        orphan.dependsOn(nativeMain)
+
+        assertEquals(CommonizerTarget(linux1.konanTarget, linux2.konanTarget), project.getCommonizerTarget(nativeMain))
+    }
+
+    @Test
+    fun `orphan source sets only`() {
+        val nativeMain = kotlin.sourceSets.create("nativeMain")
+        val orphan1 = kotlin.sourceSets.create("orphan1")
+        val orphan2 = kotlin.sourceSets.create("orphan2")
+
+        orphan1.dependsOn(nativeMain)
+        orphan2.dependsOn(nativeMain)
+
+        assertEquals(null, project.getCommonizerTarget(nativeMain))
+    }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/internal/GetCommonizerTargetOfSourceSet.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/internal/GetCommonizerTargetOfSourceSet.kt
index af0d8440e4c..54f1564c7e7 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/internal/GetCommonizerTargetOfSourceSet.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/native/internal/GetCommonizerTargetOfSourceSet.kt
@@ -13,15 +13,17 @@ import org.jetbrains.kotlin.commonizer.allLeaves
 import org.jetbrains.kotlin.gradle.dsl.multiplatformExtensionOrNull
 import org.jetbrains.kotlin.gradle.plugin.KotlinCompilation
 import org.jetbrains.kotlin.gradle.plugin.KotlinSourceSet
-import org.jetbrains.kotlin.gradle.plugin.KotlinSourceSetContainer
 import org.jetbrains.kotlin.gradle.plugin.mpp.CompilationSourceSetUtil.compilationsBySourceSets
 import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinNativeCompilation
 import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinSharedNativeCompilation
+import org.jetbrains.kotlin.gradle.plugin.sources.resolveAllSourceSetsDependingOn
 import org.jetbrains.kotlin.konan.target.KonanTarget
 
 internal fun Project.getCommonizerTarget(sourceSet: KotlinSourceSet): CommonizerTarget? {
     val kotlin = multiplatformExtensionOrNull ?: return null
-    val sourceSetsDependingOnThisSourceSet = kotlin.resolveSourceSetsDirectlyDependingOn(sourceSet)
+    val sourceSetsDependingOnThisSourceSet = kotlin.resolveAllSourceSetsDependingOn(sourceSet)
+        .filterNot(::isOrphanSourceSet)
+
     if (sourceSetsDependingOnThisSourceSet.isEmpty()) {
         return getLeafCommonizerTarget(sourceSet)
     }
@@ -50,16 +52,8 @@ private fun Project.getLeafCommonizerTarget(sourceSet: KotlinSourceSet): LeafCom
     else null
 }
 
-private fun KotlinSourceSetContainer.resolveSourceSetsDirectlyDependingOn(sourceSet: KotlinSourceSet): Set<KotlinSourceSet> {
-    val dependeeSourceSets = sourceSets
-        .filter { candidateSourceSet -> candidateSourceSet != sourceSet }
-        .filter { candidateSourceSet -> sourceSet in candidateSourceSet.dependsOn }
-
-    fun isTransitiveDependee(sourceSet: KotlinSourceSet): Boolean {
-        return sourceSet.dependsOn.any { it in dependeeSourceSets || isTransitiveDependee(it) }
-    }
-
-    return dependeeSourceSets.filterNot(::isTransitiveDependee).toSet()
+private fun Project.isOrphanSourceSet(sourceSet: KotlinSourceSet): Boolean {
+    return compilationsBySourceSets(this)[sourceSet].orEmpty().isEmpty()
 }
 
 private val KotlinCompilation<*>.konanTargets: Set<KonanTarget>
@@ -70,3 +64,4 @@ private val KotlinCompilation<*>.konanTargets: Set<KonanTarget>
             else -> emptySet()
         }
     }
+