diff --git a/src/plugins/autotoolsprojectmanager/autotoolsproject.cpp b/src/plugins/autotoolsprojectmanager/autotoolsproject.cpp
index 947b325118f..45c3f81d547 100644
--- a/src/plugins/autotoolsprojectmanager/autotoolsproject.cpp
+++ b/src/plugins/autotoolsprojectmanager/autotoolsproject.cpp
@@ -229,6 +229,7 @@ void AutotoolsProject::makefileParsingFinished()
                              f == QLatin1String("configure.ac")) ? FileType::Project : FileType::Resource,
                             false);
     });
+    rootProjectNode()->makeEmpty();
     rootProjectNode()->buildTree(fileNodes);
 
     updateCppCodeModel();
diff --git a/src/plugins/genericprojectmanager/genericproject.cpp b/src/plugins/genericprojectmanager/genericproject.cpp
index 10c61268792..7d6a12e87e3 100644
--- a/src/plugins/genericprojectmanager/genericproject.cpp
+++ b/src/plugins/genericprojectmanager/genericproject.cpp
@@ -282,6 +282,7 @@ void GenericProject::refresh(RefreshOptions options)
                                               FileType::Project,
                                               /* generated = */ false);
         fileNodes << projectFilesNode << projectIncludesNode << projectConfigNode;
+        rootProjectNode()->makeEmpty();
         rootProjectNode()->buildTree(fileNodes);
     }
 
diff --git a/src/plugins/nim/project/nimproject.cpp b/src/plugins/nim/project/nimproject.cpp
index 8f2d541f32d..74cc8a91b71 100644
--- a/src/plugins/nim/project/nimproject.cpp
+++ b/src/plugins/nim/project/nimproject.cpp
@@ -159,6 +159,7 @@ void NimProject::updateProject()
     if (oldFiles == m_files)
         return;
 
+    rootProjectNode()->makeEmpty();
     rootProjectNode()->buildTree(fileNodes);
 
     emit fileListChanged();
diff --git a/src/plugins/projectexplorer/projectnodes.cpp b/src/plugins/projectexplorer/projectnodes.cpp
index 338a279498d..542f953097d 100644
--- a/src/plugins/projectexplorer/projectnodes.cpp
+++ b/src/plugins/projectexplorer/projectnodes.cpp
@@ -478,8 +478,6 @@ FolderNode *FolderNode::recursiveFindOrCreateFolderNode(const Utils::FileName &d
 
 void FolderNode::buildTree(QList<FileNode *> &files, const Utils::FileName &overrideBaseDir)
 {
-    makeEmpty();
-
     foreach (ProjectExplorer::FileNode *fn, files) {
         // Get relative path to rootNode
         QString parentDir = fn->filePath().toFileInfo().absolutePath();
diff --git a/src/plugins/pythoneditor/pythoneditorplugin.cpp b/src/plugins/pythoneditor/pythoneditorplugin.cpp
index c3d523e1b50..d30d7e433d0 100644
--- a/src/plugins/pythoneditor/pythoneditorplugin.cpp
+++ b/src/plugins/pythoneditor/pythoneditorplugin.cpp
@@ -618,6 +618,7 @@ void PythonProject::refresh()
         const QString displayName = baseDir.relativeFilePath(f);
         return new PythonFileNode(FileName::fromString(f), displayName);
     });
+    rootProjectNode()->makeEmpty();
     rootProjectNode()->buildTree(fileNodes);
 
     emit parsingFinished();