diff --git a/kotlin-native/build.gradle b/kotlin-native/build.gradle
index e6716852ffe..59b9037a956 100644
--- a/kotlin-native/build.gradle
+++ b/kotlin-native/build.gradle
@@ -28,7 +28,6 @@ import org.jetbrains.kotlin.CompareDistributionSignatures
 import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
 import org.apache.tools.ant.filters.ReplaceTokens
 import org.jetbrains.kotlin.UtilsKt
-import java.util.concurrent.ConcurrentHashMap
 
 buildscript {
     apply from: "gradle/kotlinGradlePlugin.gradle"
@@ -96,9 +95,6 @@ ext {
 
     konanVersionFull = ext.kotlinNativeVersion
     gradlePluginVersion = konanVersionFull
-
-    // A separate map for each build for automatic cleaning the daemon after the build have finished.
-    toolClassLoadersMap = new ConcurrentHashMap<Object, URLClassLoader>()
 }
 
 allprojects {
diff --git a/kotlin-native/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/KonanToolRunner.kt b/kotlin-native/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/KonanToolRunner.kt
index 30f1527d789..6604440cb71 100644
--- a/kotlin-native/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/KonanToolRunner.kt
+++ b/kotlin-native/tools/kotlin-native-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/KonanToolRunner.kt
@@ -28,8 +28,6 @@ import java.io.File
 import java.util.Properties
 import org.jetbrains.kotlin.compilerRunner.KotlinToolRunner
 import org.jetbrains.kotlin.konan.target.AbstractToolConfig
-import java.net.URLClassLoader
-import java.util.concurrent.ConcurrentHashMap
 
 internal interface KonanToolRunner {
     fun run(args: List<String>)
@@ -70,15 +68,10 @@ internal abstract class KonanCliRunner(
             """.trimIndent()
             }
 
-    data class IsolatedClassLoaderCacheKey(val classpath: Set<File>)
+    data class IsolatedClassLoaderCacheKey(val classpath: Set<java.io.File>, val project: Project)
 
     // TODO: can't we use this for other implementations too?
-    final override val isolatedClassLoaderCacheKey get() = IsolatedClassLoaderCacheKey(classpath)
-
-    // A separate map for each build for automatic cleaning the daemon after the build have finished.
-    @Suppress("UNCHECKED_CAST")
-    final override val isolatedClassLoaders get() =
-        project.project(":kotlin-native").ext["toolClassLoadersMap"] as ConcurrentHashMap<Any, URLClassLoader>
+    final override val isolatedClassLoaderCacheKey get() = IsolatedClassLoaderCacheKey(classpath, project)
 
     override fun transformArgs(args: List<String>) = listOf(toolName) + args
 
@@ -117,9 +110,6 @@ private val load0 = Runtime::class.java.getDeclaredMethod("load0", Class::class.
 
 internal class CliToolConfig(konanHome: String, target: String) : AbstractToolConfig(konanHome, target, emptyMap()) {
     override fun loadLibclang() {
-        // Load libclang into the system class loader. This is needed to allow developers to make changes
-        // in the tooling infrastructure without having to stop the daemon (otherwise libclang might end up
-        // loaded in two different class loaders which is not allowed by the JVM).
         load0.invoke(Runtime.getRuntime(), String::class.java, libclang)
     }
 }