diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/BaseGradleIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/BaseGradleIT.kt
index 260b202fab5..dcfe8213d5e 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/BaseGradleIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/BaseGradleIT.kt
@@ -493,6 +493,13 @@ abstract class BaseGradleIT {
         return this
     }
 
+    fun CompiledProject.assertDoesNotContain(vararg notExpected: String, ignoreCase: Boolean = false): CompiledProject {
+        for (str in notExpected) {
+            assertFalse(output.contains(str.normalize(), ignoreCase), "Output should not contain '$str'")
+        }
+        return this
+    }
+
     fun CompiledProject.assertContainsRegex(expected: Regex): CompiledProject {
         assertTrue(expected.containsMatchIn(output), "Output should contain pattern '$expected'")
         return this
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MppFlagsMigrationIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MppFlagsMigrationIT.kt
index 00dd72b7bd0..8fd98719e19 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MppFlagsMigrationIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/MppFlagsMigrationIT.kt
@@ -20,6 +20,7 @@ internal class MppFlagsMigrationIT : BaseGradleIT() {
         var dependencyPropagationFlag: Boolean? = null,
         var expectedToPass: Boolean = true,
         var expectedPhraseInOutput: String? = null,
+        var notExpectedPhraseInOutput: String? = null,
     ) {
         constructor(configure: TestCase.() -> Unit) : this() {
             configure()
@@ -32,6 +33,13 @@ internal class MppFlagsMigrationIT : BaseGradleIT() {
     companion object {
         @OptIn(ExperimentalStdlibApi::class)
         private val testCases = buildList {
+            add(TestCase {
+                hierarchiesByDefault = true
+                granularMetadataFlag = null
+                dependencyPropagationFlag = null
+                expectedToPass = true
+                notExpectedPhraseInOutput = "It is safe to remove the property."
+            })
             add(TestCase {
                 hierarchiesByDefault = true
                 granularMetadataFlag = true
@@ -100,6 +108,7 @@ internal class MppFlagsMigrationIT : BaseGradleIT() {
         Project("new-mpp-published").apply {
             setupWorkingDir()
             gradleBuildScript().modify(::transformBuildScriptWithPluginsDsl)
+            gradleProperties().delete()
         }
     }
 
@@ -128,6 +137,7 @@ internal class MppFlagsMigrationIT : BaseGradleIT() {
                 assertFailed()
 
             testCase.expectedPhraseInOutput?.let { assertContains(it, ignoreCase = true) }
+            testCase.notExpectedPhraseInOutput?.let { assertDoesNotContain(it, ignoreCase = true) }
         }
     }
 }
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/hierarchicalStructureMigrationHandling.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/hierarchicalStructureMigrationHandling.kt
index 9cc02c2e5fb..cd8d5083d39 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/hierarchicalStructureMigrationHandling.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/hierarchicalStructureMigrationHandling.kt
@@ -14,11 +14,13 @@ import org.jetbrains.kotlin.gradle.utils.SingleWarningPerBuild
 import org.jetbrains.kotlin.gradle.utils.getOrPut
 
 internal fun handleHierarchicalStructureFlagsMigration(project: Project) {
-    SingleActionPerProject.run(project.rootProject, "handleHierarchicalStructureFlagsMigration - rootProject") {
-        doHandleHierarchicalStructureFlagsMigration(project.rootProject)
+    if (project.rootProject === project) {
+        SingleActionPerProject.run(project.rootProject, "handleHierarchicalStructureFlagsMigration - rootProject") {
+            doHandleHierarchicalStructureFlagsMigration(project.rootProject)
+        }
+    } else {
+        doHandleHierarchicalStructureFlagsMigration(project)
     }
-
-    doHandleHierarchicalStructureFlagsMigration(project)
 }
 
 private fun doHandleHierarchicalStructureFlagsMigration(project: Project) {