diff --git a/analysis/analysis-api-impl-base/src/org/jetbrains/kotlin/analysis/api/impl/base/util/LibraryUtils.kt b/analysis/analysis-api-impl-base/src/org/jetbrains/kotlin/analysis/api/impl/base/util/LibraryUtils.kt
index 929010107c9..b4fbae5904f 100644
--- a/analysis/analysis-api-impl-base/src/org/jetbrains/kotlin/analysis/api/impl/base/util/LibraryUtils.kt
+++ b/analysis/analysis-api-impl-base/src/org/jetbrains/kotlin/analysis/api/impl/base/util/LibraryUtils.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.analysis.api.impl.base.util
 
+import com.intellij.openapi.vfs.StandardFileSystems
 import com.intellij.openapi.vfs.VfsUtilCore
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.openapi.vfs.impl.jar.CoreJarFileSystem
@@ -22,8 +23,23 @@ object LibraryUtils {
         jar: Path,
         jarFileSystem: CoreJarFileSystem = CoreJarFileSystem(),
     ): Collection<VirtualFile> {
-        val root = jarFileSystem.refreshAndFindFileByPath(jar.toAbsolutePath().toString() + JAR_SEPARATOR)!!
+        return jarFileSystem.refreshAndFindFileByPath(jar.toAbsolutePath().toString() + JAR_SEPARATOR)
+            ?.let { getAllVirtualFilesFromRoot(it) } ?: emptySet()
+    }
 
+    /**
+     * Get all [VirtualFile]s inside the given [dir] (of [Path])
+     */
+    fun getAllVirtualFilesFromDirectory(
+        dir: Path,
+    ): Collection<VirtualFile> {
+        val fs = StandardFileSystems.local()
+        return fs.findFileByPath(dir.toAbsolutePath().toString())?.let { getAllVirtualFilesFromRoot(it) } ?: return emptySet()
+    }
+
+    private fun getAllVirtualFilesFromRoot(
+        root: VirtualFile
+    ): Collection<VirtualFile> {
         val files = mutableSetOf<VirtualFile>()
         VfsUtilCore.iterateChildrenRecursively(
             root,
diff --git a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleByCompilerConfiguration.kt b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleByCompilerConfiguration.kt
index b84358e2c84..18e512249ec 100644
--- a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleByCompilerConfiguration.kt
+++ b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleByCompilerConfiguration.kt
@@ -55,38 +55,53 @@ internal class KtSourceModuleByCompilerConfiguration(
     jarFileSystem: CoreJarFileSystem,
 ) : BaseKtModuleByCompilerConfiguration(compilerConfig, project), KtSourceModule {
     override val directRegularDependencies: List<KtModule> by lazy {
-        (compilerConfig.jvmModularRoots + compilerConfig.jvmClasspathRoots).map {
-            KtLibraryModuleByCompilerConfiguration(compilerConfig, project, it.toPath(), jarFileSystem)
+        val libraryRoots = compilerConfig.jvmModularRoots + compilerConfig.jvmClasspathRoots
+        val libraryRootsByType = libraryRoots.groupBy { it.isDirectory }
+        buildList {
+            libraryRootsByType[true]?.let { directories ->
+                directories.forEach {
+                    // E.g., project/app/build/intermediates/javac/debug/classes
+                    val root = it.toPath()
+                    val virtualFilesProvider = { LibraryUtils.getAllVirtualFilesFromDirectory(root) }
+                    add(KtLibraryModuleByCompilerConfiguration(compilerConfig, project, virtualFilesProvider, root))
+                }
+            }
+            libraryRootsByType[false]?.let { jars ->
+                jars.forEach {
+                    // E.g., project/libs/libA/a.jar
+                    val root = it.toPath()
+                    val virtualFilesProvider = { LibraryUtils.getAllVirtualFilesFromJar(root, jarFileSystem) }
+                    add(KtLibraryModuleByCompilerConfiguration(compilerConfig, project, virtualFilesProvider, root))
+                }
+            }
         }
     }
 
-    override val contentScope: GlobalSearchScope =
+    override val contentScope: GlobalSearchScope by lazy {
         TopDownAnalyzerFacadeForJVM.newModuleSearchScope(project, ktFiles)
+    }
 }
 
 internal class KtLibraryModuleByCompilerConfiguration(
     compilerConfig: CompilerConfiguration,
     project: Project,
-    private val jar: Path,
-    jarFileSystem: CoreJarFileSystem,
+    virtualFilesProvider: () -> Collection<VirtualFile>,
+    private val root: Path,
 ) : BaseKtModuleByCompilerConfiguration(compilerConfig, project), KtLibraryModule {
     override val directRegularDependencies: List<KtModule> get() = emptyList()
 
-    internal val virtualFiles: Collection<VirtualFile> by lazy {
-        LibraryUtils.getAllVirtualFilesFromJar(jar, jarFileSystem)
-    }
-
     override val libraryName: String
         get() = moduleName
 
     override val librarySources: KtLibrarySourceModule?
         get() = null
 
-    override val contentScope: GlobalSearchScope =
-        GlobalSearchScope.filesScope(project, virtualFiles)
+    override val contentScope: GlobalSearchScope by lazy {
+        GlobalSearchScope.filesScope(project, virtualFilesProvider())
+    }
 
     private val binaryRoots by lazy {
-        listOf(jar)
+        listOf(root)
     }
 
     override fun getBinaryRoots(): Collection<Path> = binaryRoots
diff --git a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/ProjectStructureProviderByCompilerConfiguration.kt b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/ProjectStructureProviderByCompilerConfiguration.kt
index 23ad2e4dbcd..528d33ba459 100644
--- a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/ProjectStructureProviderByCompilerConfiguration.kt
+++ b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/ProjectStructureProviderByCompilerConfiguration.kt
@@ -28,7 +28,7 @@ internal class ProjectStructureProviderByCompilerConfiguration(
                 val path = Paths.get(srcRoot)
                 if (Files.isDirectory(path)) {
                     // E.g., project/app/src
-                    Files.walk(Paths.get(srcRoot))
+                    Files.walk(path)
                         .filter(Files::isRegularFile)
                         .forEach { add(it.toString()) }
                 } else {
@@ -42,13 +42,12 @@ internal class ProjectStructureProviderByCompilerConfiguration(
     private val sourceModule = KtSourceModuleByCompilerConfiguration(compilerConfig, project, ktFiles, jarFileSystem)
 
     override fun getKtModuleForKtElement(element: PsiElement): KtModule {
-        val containingFilePath = element.containingFile.virtualFile.path
-        return if (containingFilePath in sourceFiles) {
+        val containingFile = element.containingFile.virtualFile
+        return if (containingFile.path in sourceFiles) {
             sourceModule
         } else {
-            sourceModule.directRegularDependencies.find { libModule ->
-                (libModule as KtLibraryModuleByCompilerConfiguration).virtualFiles.any { it.path == containingFilePath }
-            } ?: error("Can't find module for $containingFilePath")
+            sourceModule.directRegularDependencies.find { libModule -> containingFile in libModule.contentScope }
+                ?: error("Can't find module for ${containingFile.path}")
         }
     }
 }