diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.kt
index c6f1f6c50ac..7d73948e5b1 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.kt
@@ -74,13 +74,18 @@ class K2JVMCompiler : CLICompiler<K2JVMCompilerArguments>() {
         val moduleName = arguments.moduleName ?: JvmProtoBufUtil.DEFAULT_MODULE_NAME
         configuration.put(CommonConfigurationKeys.MODULE_NAME, moduleName)
 
-        configuration.configureExplicitContentRoots(arguments)
+        configuration.configureJavaModulesContentRoots(arguments)
         configuration.configureStandardLibs(paths, arguments)
         configuration.configureAdvancedJvmOptions(arguments)
         configuration.configureKlibPaths(arguments)
 
-        if (arguments.buildFile == null && !arguments.version  && !arguments.allowNoSourceFiles &&
-            (arguments.script || arguments.expression != null || arguments.freeArgs.isEmpty())) {
+        if (
+            arguments.buildFile == null &&
+            !arguments.version &&
+            !arguments.allowNoSourceFiles &&
+            (arguments.script || arguments.expression != null || arguments.freeArgs.isEmpty())
+        ) {
+            configuration.configureContentRootsFromClassPath(arguments)
 
             // script or repl
             if (arguments.script && arguments.freeArgs.isEmpty()) {
@@ -131,7 +136,7 @@ class K2JVMCompiler : CLICompiler<K2JVMCompilerArguments>() {
                 if (arguments.javaPackagePrefix != null) {
                     strongWarning("The '-Xjava-package-prefix' option is ignored because '-Xbuild-file' is specified")
                 }
-
+                configuration.configureContentRootsFromClassPath(arguments)
                 val sanitizedCollector = FilteringMessageCollector(messageCollector, VERBOSE::contains)
                 configuration.put(JVMConfigurationKeys.MODULE_XML_FILE, buildFile)
                 CompileEnvironmentUtil.loadModuleChunk(buildFile, sanitizedCollector)
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 75e0f0c7df5..9f8640fe577 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
@@ -165,10 +165,10 @@ object KotlinToJVMBytecodeCompiler {
 
         for (module in chunk) {
             for (classpathRoot in module.getClasspathRoots()) {
-                configuration.add(
-                    CLIConfigurationKeys.CONTENT_ROOTS,
-                    if (isJava9Module) JvmModulePathRoot(File(classpathRoot)) else JvmClasspathRoot(File(classpathRoot))
-                )
+                if (isJava9Module) {
+                    configuration.add(CLIConfigurationKeys.CONTENT_ROOTS, JvmModulePathRoot(File(classpathRoot)))
+                }
+                configuration.add(CLIConfigurationKeys.CONTENT_ROOTS, JvmClasspathRoot(File(classpathRoot)))
             }
         }
 
diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/jvmArguments.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/jvmArguments.kt
index 60861c8bd8e..96334961c11 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/jvmArguments.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/jvmArguments.kt
@@ -158,16 +158,13 @@ fun CompilerConfiguration.configureJdkHome(arguments: K2JVMCompilerArguments): B
     return true
 }
 
-fun CompilerConfiguration.configureExplicitContentRoots(arguments: K2JVMCompilerArguments) {
+fun CompilerConfiguration.configureJavaModulesContentRoots(arguments: K2JVMCompilerArguments) {
     for (modularRoot in arguments.javaModulePath?.split(File.pathSeparatorChar).orEmpty()) {
         add(CLIConfigurationKeys.CONTENT_ROOTS, JvmModulePathRoot(File(modularRoot)))
     }
+}
 
-    if (arguments.buildFile != null) {
-        // In the .xml compilation mode, all content roots except module path will be loaded from the .xml build file.
-        return
-    }
-
+fun CompilerConfiguration.configureContentRootsFromClassPath(arguments: K2JVMCompilerArguments) {
     for (path in arguments.classpath?.split(File.pathSeparatorChar).orEmpty()) {
         add(CLIConfigurationKeys.CONTENT_ROOTS, JvmClasspathRoot(File(path)))
     }
diff --git a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/compilationContext.kt b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/compilationContext.kt
index 38df7cf6147..cade1761e3e 100644
--- a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/compilationContext.kt
+++ b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/compilationContext.kt
@@ -269,7 +269,8 @@ private fun createInitialCompilerConfiguration(
             ScriptingCompilerConfigurationComponentRegistrar()
         )
 
-        configureExplicitContentRoots(baseArguments)
+        configureJavaModulesContentRoots(baseArguments)
+        configureContentRootsFromClassPath(baseArguments)
 
         if (!baseArguments.noStdlib) {
             addModularRootIfNotNull(isModularJava, "kotlin.stdlib", KotlinJars.stdlib)