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
new file mode 100644
index 00000000000..e52b0cd7d20
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/MppDeprecatedPropertiesIt.kt
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010-2023 JetBrains s.r.o. and Kotlin Programming Language contributors.
+ * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
+ */
+
+package org.jetbrains.kotlin.gradle.mpp
+
+import org.gradle.util.GradleVersion
+import org.jetbrains.kotlin.gradle.testbase.*
+import kotlin.io.path.appendText
+import kotlin.test.assertFalse
+import kotlin.test.assertTrue
+
+@MppGradlePluginTests
+class MppDeprecatedPropertiesIt : KGPBaseTest() {
+    @GradleTest
+    fun testDeprecations(gradleVersion: GradleVersion) {
+        project("mppDeprecatedProperties", gradleVersion) {
+            checkDeprecations(isDeprecationExpected = false)
+
+            this.gradleProperties.appendText(
+                defaultFlags.entries.joinToString(
+                    prefix = System.lineSeparator(),
+                    postfix = System.lineSeparator(),
+                    separator = System.lineSeparator(),
+                ) { (prop, value) -> "$prop=$value" }
+            )
+
+            checkDeprecations(isDeprecationExpected = true)
+        }
+    }
+
+    private fun TestProject.checkDeprecations(isDeprecationExpected: Boolean) {
+        build {
+            val assert: (Boolean, String) -> Unit = if (isDeprecationExpected) ::assertTrue else ::assertFalse
+            val warnings = output.lines().filter { it.startsWith("w:") }.toSet()
+
+            defaultFlags.keys.forEach { flag ->
+                assert(
+                    warnings.any { warning -> Regex(".*$flag.*is deprecated.*").matches(warning) },
+                    "A deprecation warning for the '$flag' should have been reported",
+                )
+            }
+        }
+    }
+
+    private val defaultFlags: Map<String, String>
+        get() = mapOf(
+            "kotlin.mpp.enableGranularSourceSetsMetadata" to "true",
+            "kotlin.mpp.enableCompatibilityMetadataVariant" to "false",
+            "kotlin.internal.mpp.hierarchicalStructureByDefault" to "true",
+            "kotlin.mpp.hierarchicalStructureSupport" to "true",
+            "kotlin.native.enableDependencyPropagation" to "false",
+        )
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/mppDeprecatedProperties/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/mppDeprecatedProperties/build.gradle.kts
new file mode 100644
index 00000000000..84ed38adf19
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/mppDeprecatedProperties/build.gradle.kts
@@ -0,0 +1,7 @@
+plugins {
+    kotlin("multiplatform")
+}
+
+kotlin {
+    jvm()
+}
diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/PropertiesProvider.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/PropertiesProvider.kt
index 2c9a684d148..56c1fd50647 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/PropertiesProvider.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/PropertiesProvider.kt
@@ -21,6 +21,7 @@ import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLI
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ANDROID_SOURCE_SET_LAYOUT_VERSION
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ANDROID_SOURCE_SET_LAYOUT_VERSION_1_NO_WARN
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_CINTEROP_COMMONIZATION
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_COMPATIBILITY_METADATA_VARIANT
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_GRANULAR_SOURCE_SETS_METADATA
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_INTRANSITIVE_METADATA_CONFIGURATION
 import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_OPTIMISTIC_NUMBER_COMMONIZATION
@@ -216,7 +217,7 @@ internal class PropertiesProvider private constructor(private val project: Proje
 
     val enableCompatibilityMetadataVariant: Boolean
         get() {
-            return (booleanProperty("kotlin.mpp.enableCompatibilityMetadataVariant") ?: !mppHierarchicalStructureByDefault)
+            return (booleanProperty(KOTLIN_MPP_ENABLE_COMPATIBILITY_METADATA_VARIANT) ?: !mppHierarchicalStructureByDefault)
         }
 
     val enableKotlinToolingMetadataArtifact: Boolean
@@ -522,7 +523,7 @@ internal class PropertiesProvider private constructor(private val project: Proje
      * 1. Project properties (-P, gradle.properties, etc...)
      * 2. `local.properties`
      */
-    private fun property(propName: String): String? =
+    internal fun property(propName: String): String? =
         if (project.hasProperty(propName)) {
             project.property(propName) as? String
         } else {
@@ -549,6 +550,7 @@ internal class PropertiesProvider private constructor(private val project: Proje
         const val KOTLIN_STDLIB_DEFAULT_DEPENDENCY = "kotlin.stdlib.default.dependency"
         const val KOTLIN_STDLIB_JDK_VARIANTS_VERSION_ALIGNMENT = "kotlin.stdlib.jdk.variants.version.alignment"
         const val KOTLIN_MPP_ENABLE_GRANULAR_SOURCE_SETS_METADATA = "kotlin.mpp.enableGranularSourceSetsMetadata"
+        const val KOTLIN_MPP_ENABLE_COMPATIBILITY_METADATA_VARIANT = "kotlin.mpp.enableCompatibilityMetadataVariant"
         const val KOTLIN_MPP_ENABLE_CINTEROP_COMMONIZATION = "kotlin.mpp.enableCInteropCommonization"
         const val KOTLIN_MPP_HIERARCHICAL_STRUCTURE_BY_DEFAULT = "kotlin.internal.mpp.hierarchicalStructureByDefault"
         const val KOTLIN_MPP_HIERARCHICAL_STRUCTURE_SUPPORT = "kotlin.mpp.hierarchicalStructureSupport"
diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/KotlinMultiplatformPlugin.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/KotlinMultiplatformPlugin.kt
index 01f137c34d0..5380718a87b 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/KotlinMultiplatformPlugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/KotlinMultiplatformPlugin.kt
@@ -22,6 +22,7 @@ import org.jetbrains.kotlin.gradle.plugin.ide.kotlinIdeMultiplatformImport
 import org.jetbrains.kotlin.gradle.plugin.ide.locateOrRegisterIdeResolveDependenciesTask
 import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinMultiplatformPlugin.Companion.sourceSetFreeCompilerArgsPropertyName
 import org.jetbrains.kotlin.gradle.plugin.mpp.apple.addBuildListenerForXcode
+import org.jetbrains.kotlin.gradle.plugin.mpp.internal.checkAndReportDeprecatedMppProperties
 import org.jetbrains.kotlin.gradle.plugin.mpp.internal.checkAndReportDeprecatedNativeTargets
 import org.jetbrains.kotlin.gradle.plugin.mpp.internal.handleHierarchicalStructureFlagsMigration
 import org.jetbrains.kotlin.gradle.plugin.mpp.pm20.*
@@ -49,6 +50,7 @@ class KotlinMultiplatformPlugin : Plugin<Project> {
     override fun apply(project: Project) {
         checkGradleCompatibility("the Kotlin Multiplatform plugin", GradleVersion.version("6.0"))
 
+        checkAndReportDeprecatedMppProperties(project)
         handleHierarchicalStructureFlagsMigration(project)
         checkAndReportDeprecatedNativeTargets(project)
 
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 1852881bd9a..d6fd72e5984 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
@@ -7,8 +7,16 @@ package org.jetbrains.kotlin.gradle.plugin.mpp.internal
 
 import org.gradle.api.Project
 import org.jetbrains.kotlin.gradle.dsl.KotlinMultiplatformExtension
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.Companion.kotlinPropertiesProvider
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_COMPATIBILITY_METADATA_VARIANT
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_ENABLE_GRANULAR_SOURCE_SETS_METADATA
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_HIERARCHICAL_STRUCTURE_BY_DEFAULT
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_MPP_HIERARCHICAL_STRUCTURE_SUPPORT
+import org.jetbrains.kotlin.gradle.plugin.PropertiesProvider.PropertyNames.KOTLIN_NATIVE_DEPENDENCY_PROPAGATION
 import org.jetbrains.kotlin.gradle.plugin.mpp.KotlinNativeTarget
+import org.jetbrains.kotlin.gradle.plugin.whenEvaluated
 import org.jetbrains.kotlin.gradle.utils.SingleWarningPerBuild
+import org.jetbrains.kotlin.gradle.utils.hasSyncErrors
 import org.jetbrains.kotlin.gradle.utils.runProjectConfigurationHealthCheckWhenEvaluated
 import org.jetbrains.kotlin.konan.target.KonanTarget
 
@@ -22,4 +30,35 @@ internal fun checkAndReportDeprecatedNativeTargets(project: Project) {
             "w: The following deprecated kotlin native targets were used in the project: ${usedDeprecatedTargets.joinToString { it.targetName }}"
         )
     }
-}
\ No newline at end of file
+}
+
+/**
+ * Declared properties have to be captured during plugin application phase before the HMPP migration util sets them.
+ * Warnings have to be reported only for successfully evaluated projects without errors.
+ */
+internal fun checkAndReportDeprecatedMppProperties(project: Project) {
+    val projectProperties = project.kotlinPropertiesProvider
+
+    val warnings = deprecatedMppProperties.mapNotNull { propertyName ->
+        projectProperties.property(propertyName)?.let { getMppDeprecationWarningMessageForProperty(propertyName) }
+    }
+
+    project.whenEvaluated {
+        if (!project.hasSyncErrors()) {
+            warnings.forEach { message ->
+                SingleWarningPerBuild.show(project, message)
+            }
+        }
+    }
+}
+
+internal val deprecatedMppProperties: List<String> = listOf(
+    KOTLIN_MPP_ENABLE_COMPATIBILITY_METADATA_VARIANT,
+    KOTLIN_MPP_ENABLE_GRANULAR_SOURCE_SETS_METADATA,
+    KOTLIN_MPP_HIERARCHICAL_STRUCTURE_BY_DEFAULT,
+    KOTLIN_MPP_HIERARCHICAL_STRUCTURE_SUPPORT,
+    KOTLIN_NATIVE_DEPENDENCY_PROPAGATION,
+)
+
+internal fun getMppDeprecationWarningMessageForProperty(property: String): String =
+    "w: The property '$property' is deprecated and is scheduled for removal in the stable Kotlin Multiplatform."
diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/utils/runProjectConfigurationHealthCheck.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/utils/runProjectConfigurationHealthCheck.kt
index 9d0453b17fb..0fe63d531e8 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/utils/runProjectConfigurationHealthCheck.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/utils/runProjectConfigurationHealthCheck.kt
@@ -60,13 +60,16 @@ import org.jetbrains.kotlin.gradle.plugin.whenEvaluated
  */
 internal inline fun Project.runProjectConfigurationHealthCheck(check: Project.() -> Unit) {
     /* Running configuration checks on a failed project will only lead to false positive error messages */
-    if (state.failure != null || (inLenientMode() && syncExceptionsAreNotEmpty())) {
+    if (project.hasSyncErrors()) {
         return
     }
 
     check()
 }
 
+internal fun Project.hasSyncErrors(): Boolean =
+    state.failure != null || (inLenientMode() && syncExceptionsAreNotEmpty())
+
 // ClassPathModeExceptionCollector is available only via 'gradleKotlinDsl()' dependency which brings in full Gradle jar
 private fun Project.syncExceptionsAreNotEmpty(): Boolean {
     val classPathModeExceptionCollectionClass = Class.forName("org.gradle.kotlin.dsl.provider.ClassPathModeExceptionCollector")