diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kotlin2JsGradlePluginIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kotlin2JsGradlePluginIT.kt
index 70d2afde2b290..2fad49e25afc3 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kotlin2JsGradlePluginIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kotlin2JsGradlePluginIT.kt
@@ -17,6 +17,7 @@ import org.jetbrains.kotlin.gradle.targets.js.npm.PackageJson
 import org.jetbrains.kotlin.gradle.targets.js.npm.fromSrcPackageJson
 import org.jetbrains.kotlin.gradle.testbase.*
 import org.jetbrains.kotlin.gradle.util.replaceText
+import org.jetbrains.kotlin.test.TestMetadata
 import org.junit.jupiter.api.DisplayName
 import java.util.zip.ZipFile
 import kotlin.io.path.*
@@ -1699,4 +1700,21 @@ class Kotlin2JsIrGradlePluginIT : KGPBaseTest() {
             }
         }
     }
+
+    @DisplayName("Check webpack update with per-file")
+    @GradleTest
+    @TestMetadata("js-per-file")
+    fun testWebpackUpdatePerFile(gradleVersion: GradleVersion) {
+        project("js-per-file", gradleVersion) {
+            build("assemble") {
+                assertTasksExecuted(":jsBrowserProductionWebpack")
+            }
+
+            projectPath.resolve("src/jsMain/kotlin/Main.kt").replaceText("CUSTOM TEXT", "CUSTOM TEXT 2")
+
+            build("assemble") {
+                assertTasksExecuted(":jsBrowserProductionWebpack")
+            }
+        }
+    }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/build.gradle.kts
new file mode 100644
index 0000000000000..c53a5eb5765b7
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/build.gradle.kts
@@ -0,0 +1,25 @@
+import org.jetbrains.kotlin.gradle.dsl.JsModuleKind
+import org.jetbrains.kotlin.gradle.targets.js.ir.KotlinJsIrLink
+
+plugins {
+    kotlin("multiplatform")
+}
+
+repositories {
+    mavenCentral()
+    mavenLocal()
+}
+
+kotlin {
+    js {
+        binaries.executable()
+        browser {
+
+        }
+    }
+}
+
+tasks.withType(KotlinJsIrLink::class.java) {
+    this.compilerOptions.freeCompilerArgs.add("-Xir-per-file")
+    this.compilerOptions.moduleKind.set(JsModuleKind.MODULE_ES)
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/Main.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/Main.kt
new file mode 100644
index 0000000000000..94da97339d170
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/Main.kt
@@ -0,0 +1,3 @@
+private fun main() {
+    SomeModule("CUSTOM TEXT")
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/SomeModule.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/SomeModule.kt
new file mode 100644
index 0000000000000..78d9d4af52533
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/js-per-file/src/jsMain/kotlin/SomeModule.kt
@@ -0,0 +1 @@
+class SomeModule(val value: String)
diff --git a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/targets/js/webpack/KotlinWebpack.kt b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/targets/js/webpack/KotlinWebpack.kt
index bc837a206fed4..6ce9c9b1ea35e 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/targets/js/webpack/KotlinWebpack.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/targets/js/webpack/KotlinWebpack.kt
@@ -38,10 +38,6 @@ import org.jetbrains.kotlin.gradle.targets.js.npm.RequiresNpmDependencies
 import org.jetbrains.kotlin.gradle.targets.js.npm.npmProject
 import org.jetbrains.kotlin.gradle.targets.js.webpack.KotlinWebpackConfig.Mode
 import org.jetbrains.kotlin.gradle.utils.*
-import org.jetbrains.kotlin.gradle.utils.archivesName
-import org.jetbrains.kotlin.gradle.utils.injected
-import org.jetbrains.kotlin.gradle.utils.property
-import org.jetbrains.kotlin.gradle.utils.providerWithLazyConvention
 import java.io.File
 import javax.inject.Inject
 
@@ -98,18 +94,19 @@ constructor(
     @get:NormalizeLineEndings
     val inputFiles: FileTree
         get() = objects.fileTree()
-            // in webpack.config.js there is path relative to npmProjectDir (kotlin/<module>.js).
-            // And we need have relative path in build cache
-            // That's why we use npmProjectDir with filter instead of just inputFilesDirectory,
-            // if we would use inputFilesDirectory, we will get in cache just file names,
-            // and if directory is changed to kotlin2, webpack config will be invalid.
-            .from(npmProjectDir)
-            .matching {
-                it.include { element: FileTreeElement ->
-                    val inputFilesDirectory = inputFilesDirectory.get().asFile
-                    element.file == inputFilesDirectory ||
-                            element.file.parentFile == inputFilesDirectory
-                }
+            .let { fileTree ->
+                val inputFilesDirectory = inputFilesDirectory.get().asFile
+                // in webpack.config.js there is path relative to npmProjectDir (kotlin/<module>.js).
+                // And we need have relative path in build cache
+                // That's why we use npmProjectDir with filter instead of just inputFilesDirectory,
+                // if we would use inputFilesDirectory, we will get in cache just file names,
+                // and if directory is changed to kotlin2, webpack config will be invalid.
+                fileTree.from(npmProjectDir)
+                    .matching {
+                        it.include { element: FileTreeElement ->
+                            inputFilesDirectory.isParentOf(element.file)
+                        }
+                    }
             }
 
     @get:Input