diff --git a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/extensions/ScriptingProcessSourcesBeforeCompilingExtension.kt b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/extensions/ScriptingProcessSourcesBeforeCompilingExtension.kt
index 28b0bed2a83..cbd0006386b 100644
--- a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/extensions/ScriptingProcessSourcesBeforeCompilingExtension.kt
+++ b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/extensions/ScriptingProcessSourcesBeforeCompilingExtension.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.scripting.compiler.plugin.extensions
 
+import com.intellij.ide.highlighter.JavaFileType
 import com.intellij.openapi.project.Project
 import org.jetbrains.kotlin.cli.common.CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY
 import org.jetbrains.kotlin.cli.common.messages.CompilerMessageSeverity
@@ -13,6 +14,7 @@ import org.jetbrains.kotlin.config.CompilerConfiguration
 import org.jetbrains.kotlin.config.LanguageFeature
 import org.jetbrains.kotlin.config.languageVersionSettings
 import org.jetbrains.kotlin.extensions.ProcessSourcesBeforeCompilingExtension
+import org.jetbrains.kotlin.idea.KotlinFileType
 import org.jetbrains.kotlin.psi.KtFile
 import org.jetbrains.kotlin.scripting.definitions.ScriptDefinitionProvider
 import org.jetbrains.kotlin.scripting.resolve.KtFileScriptSource
@@ -31,11 +33,13 @@ class ScriptingProcessSourcesBeforeCompilingExtension(val project: Project) : Pr
             return scriptDefinition?.compilationConfiguration?.get(ScriptCompilationConfiguration.isStandalone) ?: true
         }
 
+        if (configuration.getBoolean(CommonConfigurationKeys.ALLOW_ANY_SCRIPTS_IN_SOURCE_ROOTS)) return sources
+        // TODO: see comment at LazyScriptDefinitionProvider.Companion.getNonScriptFilenameSuffixes
+        val nonScriptFilenameSuffixes = arrayOf(".${KotlinFileType.EXTENSION}", ".${JavaFileType.DEFAULT_EXTENSION}")
         // filter out scripts that are not suitable for source roots, according to the compiler configuration and script definitions
         return sources.filter { ktFile ->
             when {
-                !ktFile.isScript() -> true
-                configuration.getBoolean(CommonConfigurationKeys.ALLOW_ANY_SCRIPTS_IN_SOURCE_ROOTS) -> true
+                nonScriptFilenameSuffixes.any { ktFile.virtualFilePath.endsWith(it) } -> true
                 !ktFile.isStandaloneScript() -> true
                 else -> {
                     if (!shouldSkipStandaloneScripts) {