diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/android/configurator/MultiplatformLayoutV2DefaultManifestLocationConfigurator.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/android/configurator/MultiplatformLayoutV2DefaultManifestLocationConfigurator.kt
index 3ebd4ea93a8..b6a51679d67 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/android/configurator/MultiplatformLayoutV2DefaultManifestLocationConfigurator.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/android/configurator/MultiplatformLayoutV2DefaultManifestLocationConfigurator.kt
@@ -6,14 +6,28 @@
 package org.jetbrains.kotlin.gradle.plugin.sources.android.configurator
 
 import com.android.build.gradle.api.AndroidSourceSet
+import org.gradle.api.logging.Logging
 import org.jetbrains.kotlin.gradle.plugin.KotlinSourceSet
 import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinAndroidTarget
 
 internal object MultiplatformLayoutV2DefaultManifestLocationConfigurator : KotlinAndroidSourceSetConfigurator {
+    private const val DEFAULT_FILE_NAME = "AndroidManifest.xml"
+    private val logger = Logging.getLogger(javaClass)
+
     override fun configure(target: KotlinAndroidTarget, kotlinSourceSet: KotlinSourceSet, androidSourceSet: AndroidSourceSet) {
-        /* Default can only be set when the entity is created 'fresh'. Changes here in afterEvaluate might overwrite user setup */
-        if (!target.project.state.executed) {
-            androidSourceSet.manifest.srcFile("src/${kotlinSourceSet.name}/AndroidManifest.xml")
+        val defaultManifestLocation = target.project.file("src/${androidSourceSet.name}/$DEFAULT_FILE_NAME")
+        if (androidSourceSet.manifest.srcFile != defaultManifestLocation) {
+            logger.debug(
+                """
+                    ${androidSourceSet.name}: Default Manifest location was already changed
+                    Expected: $defaultManifestLocation, Found: ${androidSourceSet.manifest.srcFile}
+                """.trimIndent()
+            )
+            return
         }
+
+        val newManifestLocation = target.project.file("src/${kotlinSourceSet.name}/$DEFAULT_FILE_NAME")
+        androidSourceSet.manifest.srcFile(newManifestLocation)
+        logger.debug("${androidSourceSet.name}: Changed default Manifest location to $newManifestLocation")
     }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/sources/android/MultiplatformAndroidSourceSetLayoutV2Test.kt b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/sources/android/MultiplatformAndroidSourceSetLayoutV2Test.kt
index bd2a0ce3cd7..e5a66efe9e7 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/sources/android/MultiplatformAndroidSourceSetLayoutV2Test.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/functionalTest/kotlin/org/jetbrains/kotlin/gradle/sources/android/MultiplatformAndroidSourceSetLayoutV2Test.kt
@@ -244,6 +244,21 @@ class MultiplatformAndroidSourceSetLayoutV2Test {
         assertEquals(project.file("custom.xml"), android.sourceSets.main.manifest.srcFile)
     }
 
+    @Test
+    fun `test - main - default Manifest location - already changed by user - does not get overwritten`() {
+        /* First: Change manifest location to something non-default */
+        val customManifestFile = project.file("src/main/CustomAndroidManifest.xml")
+        android.sourceSets.main.manifest.srcFile(customManifestFile)
+
+        /* Then: Setup Kotlin/Android target */
+        kotlin.android()
+
+        assertEquals(
+            customManifestFile, android.sourceSets.main.manifest.srcFile,
+            "Expected location of Manifest file to retain user configuration."
+        )
+    }
+
     @Test
     fun `test - defaultKotlinSourceSetName - is determined for all compilations`() {
         kotlin.android()