diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/PreHmppDependenciesDeprecationIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/PreHmppDependenciesDeprecationIT.kt
index c7c2be4457a..06fc157b094 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/PreHmppDependenciesDeprecationIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/mpp/PreHmppDependenciesDeprecationIT.kt
@@ -17,6 +17,12 @@ class PreHmppDependenciesDeprecationIT : KGPBaseTest() {
         checkDiagnostics(gradleVersion, "simpleReport", tempDir, expectReportForDependency = "preHmppLibrary")
     }
 
+    @GradleTest
+    fun testReportFromIntermediateSourceSet(gradleVersion: GradleVersion, @TempDir tempDir: Path) {
+        publishLibrary("preHmppLibrary", gradleVersion, tempDir)
+        checkDiagnostics(gradleVersion, "reportFromIntermediateSourceSet", tempDir, expectReportForDependency = "preHmppLibrary")
+    }
+
     @GradleTest
     fun testTransitiveDependencyUpgradesVersion(gradleVersion: GradleVersion, @TempDir tempDir: Path) {
         // 0.1
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/preHmppDependenciesDeprecation/reportFromIntermediateSourceSet/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/preHmppDependenciesDeprecation/reportFromIntermediateSourceSet/build.gradle.kts
new file mode 100644
index 00000000000..327105aef04
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/preHmppDependenciesDeprecation/reportFromIntermediateSourceSet/build.gradle.kts
@@ -0,0 +1,34 @@
+plugins {
+    kotlin("multiplatform")
+}
+
+repositories {
+    mavenCentral()
+    mavenLocal()
+    maven("<localRepo>")
+}
+
+kotlin {
+    jvm()
+    linuxX64()
+    js()
+
+    sourceSets {
+        val commonMain by getting
+
+        val intermediate by creating {
+            dependsOn(commonMain)
+            dependencies {
+                implementation("org.jetbrains.kotlin.tests:preHmppLibrary:0.1")
+            }
+        }
+
+        val jvmMain by getting {
+            dependsOn(intermediate)
+        }
+
+        val linuxX64Main by getting {
+            dependsOn(intermediate)
+        }
+    }
+}
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 63b89ca9d23..c8a7899b078 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
@@ -56,9 +56,9 @@ private fun reportTargetsWithNonUniqueConsumableConfigurations(project: Project)
         }
 
         SingleWarningPerBuild.show(
-            project,"w: The following targets are not distinguishable:\n$nonUniqueTargetsString" +
-            "\nUse distinguish attribute. " +
-            "See https://kotlinlang.org/docs/multiplatform-set-up-targets.html#distinguish-several-targets-for-one-platform for more details."
+            project, "w: The following targets are not distinguishable:\n$nonUniqueTargetsString" +
+                    "\nUse distinguish attribute. " +
+                    "See https://kotlinlang.org/docs/multiplatform-set-up-targets.html#distinguish-several-targets-for-one-platform for more details."
         )
     }
 }
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..18794ebf718 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
@@ -9,8 +9,10 @@ import org.gradle.api.Project
 import org.gradle.api.internal.project.ProjectInternal
 import org.gradle.api.provider.Provider
 import org.gradle.tooling.model.kotlin.dsl.KotlinDslModelsParameters
+import org.jetbrains.kotlin.gradle.plugin.KotlinPluginLifecycle
 import org.jetbrains.kotlin.gradle.plugin.internal.configurationTimePropertiesAccessor
 import org.jetbrains.kotlin.gradle.plugin.internal.usedAtConfigurationTime
+import org.jetbrains.kotlin.gradle.plugin.launchInStage
 import org.jetbrains.kotlin.gradle.plugin.whenEvaluated
 
 /**
@@ -97,7 +99,7 @@ private fun Project.inLenientMode() =
  * @see runProjectConfigurationHealthCheck
  */
 internal inline fun Project.runProjectConfigurationHealthCheckWhenEvaluated(crossinline check: Project.() -> Unit) {
-    whenEvaluated {
+    launchInStage(KotlinPluginLifecycle.Stage.ReadyForExecution) {
         runProjectConfigurationHealthCheck(check)
     }
 }