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 d1588ec4d6d..a3d73a27b3d 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
@@ -536,12 +536,13 @@ abstract class AbstractKotlin2JsGradlePluginIT(private val irBackend: Boolean) :
     }
 
     @Test
-    fun testNpmDependenciesClash() = with(Project("npm-dependencies-clash", GradleVersionRequired.AtLeast("4.10.2"))) {
+    fun testNpmDependencies() = with(Project("npm-dependencies", GradleVersionRequired.AtLeast("4.10.2"))) {
         setupWorkingDir()
         gradleBuildScript().modify(::transformBuildScriptWithPluginsDsl)
 
-        build("test") {
+        build("build") {
             assertSuccessful()
+            assertFileExists("build/js/packages/node_modules/file-dependency")
         }
     }
 
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/build.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/build.gradle.kts
similarity index 66%
rename from libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/build.gradle.kts
rename to libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/build.gradle.kts
index e3cdf39b069..a8c68ca889a 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/build.gradle.kts
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/build.gradle.kts
@@ -14,6 +14,9 @@ kotlin.sourceSets {
     getByName("main") {
         dependencies {
             implementation(kotlin("stdlib-js"))
+            // It has transitive dependency on custom github version of escodegen
+            implementation(npm("@yworks/optimizer", "1.0.6"))
+            implementation(npm("file-dependency", projectDir.resolve("file-dependency")))
         }
     }
 
@@ -21,7 +24,6 @@ kotlin.sourceSets {
         dependencies {
             implementation(kotlin("test-js"))
             implementation(npm("mocha"))
-            implementation(npm("puppeteer"))
         }
     }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/file-dependency/package.json b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/file-dependency/package.json
new file mode 100644
index 00000000000..6f2dde07aa3
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/file-dependency/package.json
@@ -0,0 +1,6 @@
+{
+  "name": "file-dependency",
+  "version": "1.0.0",
+  "main": "index.js",
+  "private": true
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/settings.gradle.kts b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/settings.gradle.kts
similarity index 69%
rename from libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/settings.gradle.kts
rename to libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/settings.gradle.kts
index 62f90a16ae4..e4ff8cae7b8 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/settings.gradle.kts
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/settings.gradle.kts
@@ -5,4 +5,4 @@ pluginManagement {
     }
 }
 
-rootProject.name = "npm-dependencies-clash"
\ No newline at end of file
+rootProject.name = "npm-dependencies"
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/src/main/kotlin/Main.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/src/main/kotlin/Main.kt
similarity index 100%
rename from libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/src/main/kotlin/Main.kt
rename to libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/src/main/kotlin/Main.kt
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/src/test/kotlin/SimpleTest.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/src/test/kotlin/SimpleTest.kt
similarity index 100%
rename from libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies-clash/src/test/kotlin/SimpleTest.kt
rename to libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/npm-dependencies/src/test/kotlin/SimpleTest.kt