diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinCompilationNpmResolver.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinCompilationNpmResolver.kt
index 9cd986597f5..23788dbfea9 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinCompilationNpmResolver.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinCompilationNpmResolver.kt
@@ -70,10 +70,6 @@ internal class KotlinCompilationNpmResolver(
 
     val projectPath = project.path
 
-    val packageJsonHandlers by lazy {
-        compilation.packageJsonHandlers
-    }
-
     @Transient
     val packageJsonTaskHolder: TaskProvider<KotlinPackageJsonTask>? =
         KotlinPackageJsonTask.create(compilation)
@@ -478,20 +474,25 @@ internal class KotlinCompilationNpmResolver(
             } else emptySet()
 
             val allNpmDependencies = externalNpmDependencies + toolsNpmDependencies + dukatIfNecessary
+            val packageJsonHandlers = if (compilationResolver.compilation != null) {
+                compilationResolver.compilation.packageJsonHandlers
+            } else {
+                compilationResolver.rootResolver.getPackageJsonHandlers(projectPath, compilationResolver.compilationDisambiguatedName)
+            }
 
             val packageJson = packageJson(
                 compilationResolver.npmProject.name,
                 compilationResolver.npmVersion,
                 compilationResolver.npmProject.main,
                 allNpmDependencies,
-                compilationResolver.packageJsonHandlers
+                packageJsonHandlers
             )
 
             compositeDependencies.forEach {
                 packageJson.dependencies[it.name] = it.version
             }
 
-            compilationResolver.packageJsonHandlers.forEach {
+            packageJsonHandlers.forEach {
                 it(packageJson)
             }
 
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolver.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolver.kt
index 2dabc244c46..8b935201c11 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolver.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolver.kt
@@ -133,14 +133,17 @@ internal class KotlinRootNpmResolver internal constructor(
         rootProject_.gradle.sharedServices.registerIfAbsent(
             KotlinRootNpmResolverStateHolder::class.qualifiedName,
             KotlinRootNpmResolverStateHolder::class.java
-        ) {
-            it.parameters.plugins.set(plugins_)
-            it.parameters.projectResolvers.set(projectResolvers_)
-            it.parameters.packageManager.set(nodeJs_.packageManager)
-            it.parameters.yarnEnvironment.set(yarnEnvironment_?.get())
-            it.parameters.npmEnvironment.set(npmEnvironment_?.get())
-            it.parameters.yarnResolutions.set(yarnResolutions_?.get())
-            it.parameters.taskRequirements.set(taskRequirements_)
+        ) { service ->
+            service.parameters.plugins.set(plugins_)
+            service.parameters.projectResolvers.set(projectResolvers_)
+            service.parameters.packageManager.set(nodeJs_.packageManager)
+            service.parameters.yarnEnvironment.set(yarnEnvironment_?.get())
+            service.parameters.npmEnvironment.set(npmEnvironment_?.get())
+            service.parameters.yarnResolutions.set(yarnResolutions_?.get())
+            service.parameters.taskRequirements.set(taskRequirements_)
+            service.parameters.packageJsonHandlers.set(compilations.associate { compilation ->
+                "${compilation.project.path}:${compilation.disambiguatedName}" to compilation.packageJsonHandlers
+            }.filter { it.value.isNotEmpty() })
         }
     }
 
@@ -197,6 +200,9 @@ internal class KotlinRootNpmResolver internal constructor(
     val compilations: Collection<KotlinJsCompilation>
         get() = projectResolvers.values.flatMap { it.compilationResolvers.map { it.compilation } }
 
+    internal fun getPackageJsonHandlers(projectPath: String, compilationDisambiguatedName: String): List<PackageJson.() -> Unit> =
+        resolverStateHolder.get().parameters.packageJsonHandlers.get()["$projectPath:$compilationDisambiguatedName"] ?: emptyList()
+
     fun findDependentResolver(src: Project, target: Project): List<KotlinCompilationNpmResolver>? {
         // todo: proper finding using KotlinTargetComponent.findUsageContext
         val targetResolver = this[target.path]
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolverStateHolder.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolverStateHolder.kt
index c36c50710ad..1d622090fd7 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolverStateHolder.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/npm/resolver/KotlinRootNpmResolverStateHolder.kt
@@ -13,6 +13,7 @@ import org.gradle.api.services.BuildServiceParameters
 import org.jetbrains.kotlin.gradle.targets.js.nodejs.TasksRequirements
 import org.jetbrains.kotlin.gradle.targets.js.npm.NpmApi
 import org.jetbrains.kotlin.gradle.targets.js.npm.NpmEnvironment
+import org.jetbrains.kotlin.gradle.targets.js.npm.PackageJson
 import org.jetbrains.kotlin.gradle.targets.js.npm.plugins.RootResolverPlugin
 import org.jetbrains.kotlin.gradle.targets.js.yarn.YarnEnv
 import org.jetbrains.kotlin.gradle.targets.js.yarn.YarnResolution
@@ -27,6 +28,9 @@ internal abstract class KotlinRootNpmResolverStateHolder : BuildService<KotlinRo
         val npmEnvironment: Property<NpmEnvironment>
         val yarnResolutions: ListProperty<YarnResolution>
         val taskRequirements: Property<TasksRequirements>
+
+        // pulled up from compilation resolver since it was failing with ClassNotFoundException on deserialization, see KT-49061
+        val packageJsonHandlers: MapProperty<String, List<PackageJson.() -> Unit>>
     }
 
     var initialized = false