diff --git a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/ir/CirAnnotation.kt b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/ir/CirAnnotation.kt
index e8001fcf74a..edb27b49e84 100644
--- a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/ir/CirAnnotation.kt
+++ b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/ir/CirAnnotation.kt
@@ -7,9 +7,10 @@ package org.jetbrains.kotlin.descriptors.commonizer.mergedtree.ir
 
 import org.jetbrains.kotlin.descriptors.annotations.AnnotationDescriptor
 import org.jetbrains.kotlin.descriptors.commonizer.utils.Interner
-import org.jetbrains.kotlin.descriptors.commonizer.utils.appendHashCode
 import org.jetbrains.kotlin.descriptors.commonizer.utils.hashCode
+import org.jetbrains.kotlin.descriptors.commonizer.utils.appendHashCode
 import org.jetbrains.kotlin.descriptors.commonizer.utils.intern
+import org.jetbrains.kotlin.descriptors.commonizer.utils.isUnderStandardKotlinPackages
 import org.jetbrains.kotlin.name.FqName
 import org.jetbrains.kotlin.name.Name
 import org.jetbrains.kotlin.resolve.constants.*
@@ -64,6 +65,12 @@ internal fun checkSupportedInCommonization(constantValue: ConstantValue<*>, loca
         is EnumValue -> {
             // OK
         }
+        is AnnotationValue -> {
+            if (constantValue.value.fqName?.isUnderStandardKotlinPackages != true)
+                error("Only ${constantValue::class.java} const values from Kotlin standard packages are supported, $constantValue at ${location()}")
+
+            Unit
+        }
         is ArrayValue -> {
             constantValue.value.forEachIndexed { index, innerConstantValue ->
                 checkSupportedInCommonization(innerConstantValue) { "${location()}[$index]" }
diff --git a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/memberScopes.kt b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/memberScopes.kt
index e796a57b68a..97848bb385b 100644
--- a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/memberScopes.kt
+++ b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/mergedtree/memberScopes.kt
@@ -10,7 +10,7 @@ import org.jetbrains.kotlin.descriptors.commonizer.core.Commonizer
 import org.jetbrains.kotlin.descriptors.commonizer.utils.*
 import org.jetbrains.kotlin.descriptors.commonizer.utils.fqNameWithTypeParameters
 import org.jetbrains.kotlin.descriptors.commonizer.utils.isBlacklistedDarwinFunction
-import org.jetbrains.kotlin.descriptors.commonizer.utils.isDeprecated
+import org.jetbrains.kotlin.descriptors.commonizer.utils.isDeprecatedTopLevelFunction
 import org.jetbrains.kotlin.descriptors.commonizer.utils.isKniBridgeFunction
 import org.jetbrains.kotlin.name.Name
 import org.jetbrains.kotlin.resolve.scopes.MemberScope
@@ -57,7 +57,7 @@ internal inline fun FunctionCollector(
 ): (DeclarationDescriptor) -> Boolean = Collector<SimpleFunctionDescriptor> { candidate ->
     if (candidate.kind.isReal
         && !candidate.isKniBridgeFunction()
-        && !candidate.isDeprecated()
+        && !candidate.isDeprecatedTopLevelFunction()
         && !candidate.isBlacklistedDarwinFunction()
     ) {
         typedCollector(candidate)
diff --git a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/utils/blacklist.kt b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/utils/blacklist.kt
index c089090d4e2..b59109b6a37 100644
--- a/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/utils/blacklist.kt
+++ b/native/commonizer/src/org/jetbrains/kotlin/descriptors/commonizer/utils/blacklist.kt
@@ -15,8 +15,8 @@ private val DEPRECATED_ANNOTATION_FQN = FqName(Deprecated::class.java.name)
 internal fun SimpleFunctionDescriptor.isKniBridgeFunction() =
     name.asString().startsWith("kniBridge")
 
-internal fun SimpleFunctionDescriptor.isDeprecated() =
-    annotations.hasAnnotation(DEPRECATED_ANNOTATION_FQN)
+internal fun SimpleFunctionDescriptor.isDeprecatedTopLevelFunction() =
+    containingDeclaration is PackageFragmentDescriptor && annotations.hasAnnotation(DEPRECATED_ANNOTATION_FQN)
 
 // the following logic determines Kotlin functions with conflicting overloads in Darwin library:
 internal fun SimpleFunctionDescriptor.isBlacklistedDarwinFunction(): Boolean {
diff --git a/native/commonizer/testData/functionCommonization/specifics/commonized/common/package_root.kt b/native/commonizer/testData/functionCommonization/specifics/commonized/common/package_root.kt
index 43d5aa82a9f..4711ca2507e 100644
--- a/native/commonizer/testData/functionCommonization/specifics/commonized/common/package_root.kt
+++ b/native/commonizer/testData/functionCommonization/specifics/commonized/common/package_root.kt
@@ -16,3 +16,8 @@ expect fun externalFunction2()
 
 expect inline fun inlineFunction1() {}
 expect fun inlineFunction2() {}
+
+expect class Holder() {
+    expect fun deprecatedFunction1()
+    expect fun nonDeprecatedFunction1()
+}
diff --git a/native/commonizer/testData/functionCommonization/specifics/commonized/js/package_root.kt b/native/commonizer/testData/functionCommonization/specifics/commonized/js/package_root.kt
index b4d1d29b05b..c07798f3e7d 100644
--- a/native/commonizer/testData/functionCommonization/specifics/commonized/js/package_root.kt
+++ b/native/commonizer/testData/functionCommonization/specifics/commonized/js/package_root.kt
@@ -17,3 +17,13 @@ actual external fun externalFunction2()
 
 actual inline fun inlineFunction1() {}
 actual inline fun inlineFunction2() {}
+
+actual class Holder actual constructor() {
+    @Deprecated("This function is deprecated")
+    actual fun deprecatedFunction1() {}
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction2() {}
+
+    actual fun nonDeprecatedFunction1() {}
+    fun nonDeprecatedFunction2() {}
+}
diff --git a/native/commonizer/testData/functionCommonization/specifics/commonized/jvm/package_root.kt b/native/commonizer/testData/functionCommonization/specifics/commonized/jvm/package_root.kt
index 9559cf2288a..0eb81473183 100644
--- a/native/commonizer/testData/functionCommonization/specifics/commonized/jvm/package_root.kt
+++ b/native/commonizer/testData/functionCommonization/specifics/commonized/jvm/package_root.kt
@@ -17,3 +17,13 @@ actual fun externalFunction2() {}
 
 actual inline fun inlineFunction1() {}
 actual fun inlineFunction2() {}
+
+actual class Holder actual constructor() {
+    @Deprecated("This function is deprecated")
+    actual fun deprecatedFunction1() {}
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction3() {}
+
+    actual fun nonDeprecatedFunction1() {}
+    fun nonDeprecatedFunction3() {}
+}
diff --git a/native/commonizer/testData/functionCommonization/specifics/original/js/package_root.kt b/native/commonizer/testData/functionCommonization/specifics/original/js/package_root.kt
index b7be16676e1..b0580e2367c 100644
--- a/native/commonizer/testData/functionCommonization/specifics/original/js/package_root.kt
+++ b/native/commonizer/testData/functionCommonization/specifics/original/js/package_root.kt
@@ -18,7 +18,17 @@ external fun externalFunction2()
 inline fun inlineFunction1() {}
 inline fun inlineFunction2() {}
 
-@Deprecated
+@Deprecated("This function is deprecated")
 fun deprecatedFunction1() {}
-@Deprecated
+@Deprecated("This function is deprecated")
 fun deprecatedFunction2() {}
+
+class Holder {
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction1() {}
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction2() {}
+
+    fun nonDeprecatedFunction1() {}
+    fun nonDeprecatedFunction2() {}
+}
diff --git a/native/commonizer/testData/functionCommonization/specifics/original/jvm/package_root.kt b/native/commonizer/testData/functionCommonization/specifics/original/jvm/package_root.kt
index 58f31ed2baf..9bd00b7f5fa 100644
--- a/native/commonizer/testData/functionCommonization/specifics/original/jvm/package_root.kt
+++ b/native/commonizer/testData/functionCommonization/specifics/original/jvm/package_root.kt
@@ -18,7 +18,17 @@ fun externalFunction2() {}
 inline fun inlineFunction1() {}
 fun inlineFunction2() {}
 
-@Deprecated
+@Deprecated("This function is deprecated")
 fun deprecatedFunction1() {}
-@Deprecated
+@Deprecated("This function is deprecated")
 fun deprecatedFunction3() {}
+
+class Holder {
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction1() {}
+    @Deprecated("This function is deprecated")
+    fun deprecatedFunction3() {}
+
+    fun nonDeprecatedFunction1() {}
+    fun nonDeprecatedFunction3() {}
+}