diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
index 6b3fad6b4bd..fd986e4904b 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
@@ -350,7 +350,7 @@ class KotlinCoreEnvironment private constructor(
 
     fun updateClasspath(contentRoots: List<ContentRoot>): List<File>? {
         // TODO: add new Java modules to CliJavaModuleResolver
-        val newRoots = classpathRootsResolver.convertClasspathRoots(contentRoots).roots
+        val newRoots = classpathRootsResolver.convertClasspathRoots(contentRoots).roots - initialRoots
 
         if (packagePartProviders.isEmpty()) {
             initialRoots.addAll(newRoots)