diff --git a/python/ide/impl/src/com/jetbrains/python/newProject/steps/PythonBaseProjectGenerator.java b/python/ide/impl/src/com/jetbrains/python/newProject/steps/PythonBaseProjectGenerator.java
index bb914ff232cb..d890baf090a2 100644
--- a/python/ide/impl/src/com/jetbrains/python/newProject/steps/PythonBaseProjectGenerator.java
+++ b/python/ide/impl/src/com/jetbrains/python/newProject/steps/PythonBaseProjectGenerator.java
@@ -56,7 +56,7 @@ public final class PythonBaseProjectGenerator extends PythonProjectGenerator<PyN
     // Super should be called according to its contract unless we sync project explicitly (we do not, so we call super)
     super.configureProject(project, baseDir, settings, module, synchronizer);
     PySdkExtKt.setPythonSdk(module, settings.getSdk());
-    PyWelcomeGenerator.INSTANCE.welcomeUser(project, baseDir);
+    PyWelcomeGenerator.INSTANCE.welcomeUser(project, baseDir, module);
   }
 
   @NotNull
diff --git a/python/ide/impl/src/com/jetbrains/python/newProject/welcome/PyWelcome.kt b/python/ide/impl/src/com/jetbrains/python/newProject/welcome/PyWelcome.kt
index b391be201e75..d74bfd74343b 100644
--- a/python/ide/impl/src/com/jetbrains/python/newProject/welcome/PyWelcome.kt
+++ b/python/ide/impl/src/com/jetbrains/python/newProject/welcome/PyWelcome.kt
@@ -24,6 +24,7 @@ import com.intellij.openapi.ui.CheckBoxWithDescription
 import com.intellij.openapi.util.Disposer
 import com.intellij.openapi.util.Ref
 import com.intellij.openapi.util.SystemInfo
+import com.intellij.openapi.vfs.VfsUtil
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.openapi.wm.ToolWindowId
 import com.intellij.openapi.wm.ToolWindowManager.Companion.getInstance
@@ -40,6 +41,7 @@ import com.jetbrains.python.newProject.welcome.PyWelcomeCollector.Companion.Proj
 import com.jetbrains.python.newProject.welcome.PyWelcomeCollector.Companion.ScriptResult
 import com.jetbrains.python.psi.LanguageLevel
 import com.jetbrains.python.run.PythonRunConfigurationProducer
+import com.jetbrains.python.sdk.pythonSdk
 import org.jetbrains.annotations.CalledInAny
 import org.jetbrains.concurrency.CancellablePromise
 import java.awt.event.ItemEvent
@@ -55,7 +57,7 @@ internal class PyWelcomeConfigurator : DirectoryProjectConfigurator {
     }
 
     StartupManager.getInstance(project).runAfterOpened {
-      PyWelcome.welcomeUser(project, baseDir, false)
+      PyWelcome.welcomeUser(project, baseDir, moduleRef.get(), false)
     }
   }
 }
@@ -71,8 +73,8 @@ internal object PyWelcomeGenerator {
     )
   }
 
-  fun welcomeUser(project: Project, baseDir: VirtualFile) {
-    PyWelcome.welcomeUser(project, baseDir, true)
+  fun welcomeUser(project: Project, baseDir: VirtualFile, module: Module) {
+    PyWelcome.welcomeUser(project, baseDir, module, true)
   }
 }
 
@@ -80,15 +82,13 @@ private object PyWelcome {
   private val LOG = Logger.getInstance(PyWelcome::class.java)
 
   @CalledInAny
-  fun welcomeUser(project: Project, baseDir: VirtualFile, newProject: Boolean) {
+  fun welcomeUser(project: Project, baseDir: VirtualFile, module: Module?, newProject: Boolean) {
     val enabled = PyWelcomeSettings.instance.createWelcomeScriptForEmptyProject
 
-    if (enabled) {
-      PyWelcomeCollector.logWelcomeProject(project, if (newProject) ProjectType.NEW else ProjectType.OPENED)
-    }
+    PyWelcomeCollector.logWelcomeProject(project, if (newProject) ProjectType.NEW else ProjectType.OPENED)
 
     if (enabled &&
-        isEmptyProject(baseDir).also { if (!it) PyWelcomeCollector.logWelcomeScript(project, ScriptResult.NOT_EMPTY) }) {
+        isEmptyProject(project, baseDir, module).also { if (!it) PyWelcomeCollector.logWelcomeScript(project, ScriptResult.NOT_EMPTY) }) {
       prepareFileAndOpen(project, baseDir).onSuccess {
         if (it != null) {
           // expand tree after the welcome script is created, otherwise expansion will have no effect on empty tree
@@ -102,8 +102,14 @@ private object PyWelcome {
     }
   }
 
-  private fun isEmptyProject(baseDir: VirtualFile): Boolean {
-    return baseDir.children.all { ProjectCoreUtil.isProjectOrWorkspaceFile(it) }
+  private fun isEmptyProject(project: Project, baseDir: VirtualFile, module: Module?): Boolean {
+    val sdkBinary = (module?.pythonSdk ?: project.pythonSdk)?.homeDirectory
+    val innerSdk = sdkBinary != null && VfsUtil.isAncestor(baseDir, sdkBinary, true)
+
+    return baseDir.children.all {
+      ProjectCoreUtil.isProjectOrWorkspaceFile(it) ||
+      (innerSdk && it.isDirectory && VfsUtil.isAncestor(it, sdkBinary!!, true))
+    }
   }
 
   private fun prepareFileAndOpen(project: Project, baseDir: VirtualFile): CancellablePromise<PsiFile?> {
@@ -132,6 +138,8 @@ private object PyWelcome {
 
   @CalledInAny
   private fun expandProjectTree(project: Project) {
+    // the approach was taken from com.intellij.platform.PlatformProjectViewOpener
+
     val toolWindow = getInstance(project).getToolWindow(ToolWindowId.PROJECT_VIEW)
     if (toolWindow == null) {
       val listener = ProjectViewListener(project)