diff --git a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/unitTests/CInteropCommonizerConfigurationTests.kt b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/unitTests/CInteropCommonizerConfigurationTests.kt
index ca50f9fbe1d..417eba6eb52 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/unitTests/CInteropCommonizerConfigurationTests.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/unitTests/CInteropCommonizerConfigurationTests.kt
@@ -7,14 +7,24 @@
 
 package org.jetbrains.kotlin.gradle.unitTests
 
+import org.gradle.api.artifacts.Configuration
+import org.gradle.api.artifacts.ProjectDependency
 import org.gradle.kotlin.dsl.dependencies
 import org.jetbrains.kotlin.commonizer.CommonizerTarget
 import org.jetbrains.kotlin.commonizer.identityString
+import org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformSourceSetConventionsImpl.commonMain
+import org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformSourceSetConventionsImpl.linuxMain
+import org.jetbrains.kotlin.gradle.dsl.multiplatformExtension
+import org.jetbrains.kotlin.gradle.plugin.KotlinPluginLifecycle
+import org.jetbrains.kotlin.gradle.plugin.KotlinPluginLifecycle.Stage.ReadyForExecution
+import org.jetbrains.kotlin.gradle.plugin.await
 import org.jetbrains.kotlin.gradle.targets.native.internal.CommonizerTargetAttribute
-import org.jetbrains.kotlin.gradle.util.buildProjectWithMPP
+import org.jetbrains.kotlin.gradle.targets.native.internal.locateOrCreateCommonizedCInteropDependencyConfiguration
+import org.jetbrains.kotlin.gradle.util.*
 import org.jetbrains.kotlin.gradle.utils.markConsumable
 import org.jetbrains.kotlin.gradle.utils.markResolvable
 import org.jetbrains.kotlin.konan.target.KonanTarget
+import org.jetbrains.kotlin.tooling.core.UnsafeApi
 import kotlin.test.Test
 import kotlin.test.assertEquals
 import kotlin.test.fail
@@ -114,4 +124,72 @@ class CInteropCommonizerConfigurationTests {
         val resolved = resolvedDependencies.single()
         assertEquals(consumableSpecific.name, resolved.configuration)
     }
+
+    @Test
+    fun `test - KT-63338 - source sets have own cinterop configurations`() {
+        val rootProject = buildProject()
+
+        val producerAProject = buildProjectWithMPP(
+            projectBuilder = { withParent(rootProject).withName("producer-a") }
+        ) {
+            kotlin {
+                linuxX64().compilations.main.cinterops.create("myInterop")
+                linuxArm64().compilations.main.cinterops.create("myInterop")
+            }
+        }
+
+        val producerBProject = buildProjectWithMPP(
+            projectBuilder = { withParent(rootProject).withName("producer-b") }
+        ) {
+            kotlin {
+                linuxX64().compilations.main.cinterops.create("myInterop")
+                linuxArm64().compilations.main.cinterops.create("myInterop")
+            }
+        }
+
+
+        val consumerProject = buildProjectWithMPP(
+            projectBuilder = { withParent(rootProject).withName("consumer") }
+        ) {
+            kotlin {
+                linuxX64()
+                linuxArm64()
+
+                sourceSets.commonMain.dependencies {
+                    implementation(project(":producer-a"))
+                }
+
+                sourceSets.linuxMain.dependencies {
+                    implementation(project(":producer-b"))
+                }
+            }
+        }
+
+        producerAProject.evaluate()
+
+        consumerProject.runLifecycleAwareTest {
+            val commonMain = consumerProject.multiplatformExtension.sourceSets.commonMain
+            val linuxMain = consumerProject.multiplatformExtension.sourceSets.linuxMain
+
+            @OptIn(UnsafeApi::class)
+            val commonMainCinterop = consumerProject.locateOrCreateCommonizedCInteropDependencyConfiguration(commonMain.get())!!
+
+            @OptIn(UnsafeApi::class)
+            val linuxMainCinterop = consumerProject.locateOrCreateCommonizedCInteropDependencyConfiguration(linuxMain.get())!!
+
+            if (linuxMainCinterop == commonMainCinterop)
+                fail("Expected different source sets have different resolvable Cinterop configurations")
+
+            fun Configuration.allProjectDependencies() = allDependencies
+                .filterIsInstance<ProjectDependency>()
+                .map { it.dependencyProject }
+                .toSet()
+
+            if (commonMainCinterop.allProjectDependencies() != setOf(producerAProject))
+                fail("commonMain Cinterop configuration should depend only on `producer-a` project")
+
+            if (linuxMainCinterop.allProjectDependencies() != setOf(producerAProject, producerBProject))
+                fail("linuxMain Cinterop configuration should depend on both `producer-a` and `producer-b` projects")
+        }
+    }
 }
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