diff --git a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/builder/KtSourceModuleBuilder.kt b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/builder/KtSourceModuleBuilder.kt
index 1f5e17993a7..9234300bb58 100644
--- a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/builder/KtSourceModuleBuilder.kt
+++ b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/builder/KtSourceModuleBuilder.kt
@@ -5,18 +5,22 @@
 
 package org.jetbrains.kotlin.analysis.project.structure.builder
 
-import com.intellij.psi.PsiFileSystemItem
+import com.intellij.openapi.vfs.VirtualFile
+import com.intellij.psi.PsiManager
 import com.intellij.psi.search.GlobalSearchScope
 import org.jetbrains.kotlin.analysis.project.structure.KtSourceModule
 import org.jetbrains.kotlin.analysis.project.structure.impl.KtSourceModuleImpl
+import org.jetbrains.kotlin.analysis.project.structure.impl.collectSourceFilePaths
 import org.jetbrains.kotlin.cli.jvm.compiler.KotlinCoreProjectEnvironment
 import org.jetbrains.kotlin.config.ApiVersion
 import org.jetbrains.kotlin.config.LanguageVersion
 import org.jetbrains.kotlin.config.LanguageVersionSettings
 import org.jetbrains.kotlin.config.LanguageVersionSettingsImpl
+import java.nio.file.Path
 import kotlin.contracts.ExperimentalContracts
 import kotlin.contracts.InvocationKind
 import kotlin.contracts.contract
+import kotlin.io.path.isDirectory
 
 @KtModuleBuilderDsl
 public class KtSourceModuleBuilder(
@@ -25,19 +29,22 @@ public class KtSourceModuleBuilder(
     public lateinit var moduleName: String
     public var languageVersionSettings: LanguageVersionSettings =
         LanguageVersionSettingsImpl(LanguageVersion.LATEST_STABLE, ApiVersion.LATEST)
-    public lateinit var contentScope: GlobalSearchScope
 
-    private val sourceRoots: MutableList<PsiFileSystemItem> = mutableListOf()
+    private val sourceRoots: MutableList<Path> = mutableListOf()
 
-    public fun addSourceRoot(file: PsiFileSystemItem) {
-        sourceRoots.add(file)
+    public fun addSourceRoot(path: Path) {
+        sourceRoots.add(path)
     }
 
-    public fun addSourceRoots(files: Collection<PsiFileSystemItem>) {
-        sourceRoots.addAll(files)
+    public fun addSourceRoots(paths: Collection<Path>) {
+        sourceRoots.addAll(paths)
     }
 
     override fun build(): KtSourceModule {
+        val virtualFiles = collectVirtualFilesByRoots()
+        val psiManager = PsiManager.getInstance(kotlinCoreProjectEnvironment.project)
+        val psiFiles = virtualFiles.mapNotNull { psiManager.findFile(it) }
+        val contentScope = GlobalSearchScope.filesScope(kotlinCoreProjectEnvironment.project, virtualFiles)
         return KtSourceModuleImpl(
             directRegularDependencies,
             directDependsOnDependencies,
@@ -47,9 +54,26 @@ public class KtSourceModuleBuilder(
             kotlinCoreProjectEnvironment.project,
             moduleName,
             languageVersionSettings,
-            sourceRoots,
+            psiFiles,
         )
     }
+
+    private fun collectVirtualFilesByRoots(): List<VirtualFile> {
+        val localFileSystem = kotlinCoreProjectEnvironment.environment.localFileSystem
+        return buildList {
+            for (root in sourceRoots) {
+                val files = if (root.isDirectory()) {
+                    collectSourceFilePaths(root)
+                } else {
+                    listOf(root)
+                }
+                for (file in files) {
+                    val virtualFile = localFileSystem.findFileByIoFile(file.toFile()) ?: continue
+                    add(virtualFile)
+                }
+            }
+        }
+    }
 }
 
 @OptIn(ExperimentalContracts::class)
diff --git a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleUtils.kt b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleUtils.kt
index 95a3a4884e4..316836bdcfe 100644
--- a/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleUtils.kt
+++ b/analysis/analysis-api-standalone/src/org/jetbrains/kotlin/analysis/project/structure/impl/KtModuleUtils.kt
@@ -15,7 +15,6 @@ import org.jetbrains.kotlin.analysis.api.standalone.base.project.structure.KtSta
 import org.jetbrains.kotlin.analysis.project.structure.builder.*
 import org.jetbrains.kotlin.analyzer.common.CommonPlatformAnalyzerServices
 import org.jetbrains.kotlin.cli.jvm.compiler.KotlinCoreProjectEnvironment
-import org.jetbrains.kotlin.cli.jvm.compiler.TopDownAnalyzerFacadeForJVM
 import org.jetbrains.kotlin.cli.jvm.config.javaSourceRoots
 import org.jetbrains.kotlin.cli.jvm.config.jvmClasspathRoots
 import org.jetbrains.kotlin.cli.jvm.config.jvmModularRoots
@@ -67,7 +66,7 @@ internal fun getSourceFilePaths(
             val path = Paths.get(srcRoot)
             if (Files.isDirectory(path)) {
                 // E.g., project/app/src
-                collectSourceFilePaths(path, this)
+                addAll(collectSourceFilePaths(path))
                 if (includeDirectoryRoot) {
                     add(path)
                 }
@@ -80,19 +79,17 @@ internal fun getSourceFilePaths(
 }
 
 /**
- * Collect source file path from the given [root] store them in [result].
+ * Collect source file path from the given [root]
  *
  * E.g., for `project/app/src` as a [root], this will walk the file tree and
  * collect all `.kt`, `.kts`, and `.java` files under that folder.
  *
  * Note that this util gracefully skips [IOException] during file tree traversal.
  */
-private fun collectSourceFilePaths(
-    root: Path,
-    result: MutableSet<Path>
-) {
+internal fun collectSourceFilePaths(root: Path): List<Path> {
     // NB: [Files#walk] throws an exception if there is an issue during IO.
     // With [Files#walkFileTree] with a custom visitor, we can take control of exception handling.
+    val result = mutableListOf<Path>()
     Files.walkFileTree(
         root,
         object : SimpleFileVisitor<Path>() {
@@ -125,6 +122,7 @@ private fun collectSourceFilePaths(
             }
         }
     )
+    return result
 }
 
 internal inline fun <reified T : PsiFileSystemItem> getPsiFilesFromPaths(
@@ -197,13 +195,7 @@ internal fun buildKtModuleProviderByCompilerConfiguration(
 
         addModuleDependencies(moduleName)
 
-        contentScope = TopDownAnalyzerFacadeForJVM.newModuleSearchScope(kotlinCoreProjectEnvironment.project, ordinaryFiles)
-        addSourceRoots(
-            getPsiFilesFromPaths(
-                kotlinCoreProjectEnvironment,
-                getSourceFilePaths(compilerConfig, includeDirectoryRoot = true)
-            )
-        )
+        addSourceRoots(compilerConfig.javaSourceRoots.map { Paths.get(it) })
     }.apply(::addModule)