diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/MppDeprecatedPropertiesIt.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/MppDeprecatedPropertiesIt.kt
index 84f632125b0..579346fdaba 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/MppDeprecatedPropertiesIt.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/MppDeprecatedPropertiesIt.kt
@@ -8,6 +8,7 @@ package org.jetbrains.kotlin.gradle.mpp
 import org.gradle.util.GradleVersion
 import org.jetbrains.kotlin.gradle.testbase.*
 import kotlin.io.path.appendText
+import kotlin.io.path.writeText
 import kotlin.test.assertFalse
 import kotlin.test.assertTrue
 
@@ -27,6 +28,10 @@ class MppDeprecatedPropertiesIt : KGPBaseTest() {
             )
             checkDeprecations(isDeprecationExpected = true)
 
+            // remove the MPP plugin from the top-level project and check the warnings are still reported in subproject
+            this.buildGradleKts.writeText("")
+            checkDeprecations(isDeprecationExpected = true)
+
             this.gradleProperties.appendText("kotlin.mpp.deprecatedProperties.nowarn=true${System.lineSeparator()}")
             checkDeprecations(isDeprecationExpected = false)
         }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/deprecationDiagnostics.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/deprecationDiagnostics.kt
index a0fd02168de..4a6d2e39661 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/deprecationDiagnostics.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/internal/deprecationDiagnostics.kt
@@ -38,12 +38,13 @@ internal fun checkAndReportDeprecatedNativeTargets(project: Project) {
  * Warnings have to be reported only for successfully evaluated projects without errors.
  */
 internal fun checkAndReportDeprecatedMppProperties(project: Project) {
-    if (project !== project.rootProject) return
-
     val projectProperties = project.kotlinPropertiesProvider
     if (projectProperties.ignoreHmppDeprecationWarnings == true) return
 
     val warnings = deprecatedMppProperties.mapNotNull { propertyName ->
+        if (propertyName in propertiesSetByPlugin && projectProperties.mpp13XFlagsSetByPlugin)
+            return@mapNotNull null
+
         @OptIn(UnsafeApi::class)
         projectProperties.property(propertyName)?.let { getMppDeprecationWarningMessageForProperty(propertyName) }
     }
@@ -65,6 +66,11 @@ internal val deprecatedMppProperties: List<String> = listOf(
     KOTLIN_NATIVE_DEPENDENCY_PROPAGATION,
 )
 
+private val propertiesSetByPlugin: Set<String> = setOf(
+    KOTLIN_MPP_ENABLE_GRANULAR_SOURCE_SETS_METADATA,
+    KOTLIN_NATIVE_DEPENDENCY_PROPAGATION,
+)
+
 internal fun getMppDeprecationWarningMessageForProperty(property: String): String =
     "w: The property '$property' is obsolete and will be removed in Kotlin 1.9. Read the details here: " +
             "https://kotlinlang.org/docs/multiplatform-compatibility-guide.html#deprecate-hmpp-properties"