diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
index 8e3e4f4c594..64b3f5b1bf5 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
@@ -512,7 +512,11 @@ fun CompilerConfiguration.configureSourceRoots(chunk: List<Module>, buildFile: F
         val commonSources = getBuildFilePaths(buildFile, module.getCommonSourceFiles()).toSet()
 
         for (path in getBuildFilePaths(buildFile, module.getSourceFiles())) {
-            addKotlinSourceRoot(path, isCommon = path in commonSources, hmppCliModuleStructure?.getModuleNameForSource(path))
+            addKotlinSourceRoot(
+                path,
+                isCommon = hmppCliModuleStructure?.isFromCommonModule(path) ?: (path in commonSources),
+                hmppCliModuleStructure?.getModuleNameForSource(path)
+            )
         }
     }
 
diff --git a/compiler/config/src/org/jetbrains/kotlin/config/HmppCliModule.kt b/compiler/config/src/org/jetbrains/kotlin/config/HmppCliModule.kt
index 384a0cceadd..4dc6be79386 100644
--- a/compiler/config/src/org/jetbrains/kotlin/config/HmppCliModule.kt
+++ b/compiler/config/src/org/jetbrains/kotlin/config/HmppCliModule.kt
@@ -23,3 +23,7 @@ class HmppCliModuleStructure(
 fun HmppCliModuleStructure.getModuleNameForSource(source: String): String? {
     return modules.firstOrNull { source in it.sources }?.name
 }
+
+fun HmppCliModuleStructure.isFromCommonModule(source: String): Boolean {
+    return modules.indexOfFirst { source in it.sources }.let { it >= 0 && it < modules.size - 1 }
+}