diff --git a/src/file/indexcleaner.cpp b/src/file/indexcleaner.cpp
index e5ab85a4..4ff96368 100644
--- a/src/file/indexcleaner.cpp
+++ b/src/file/indexcleaner.cpp
@@ -1,90 +1,92 @@
 /*
  * Copyright (C) 2015  Vishesh Handa <vhanda@kde.org>
  *
  * This library is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public
  * License as published by the Free Software Foundation; either
  * version 2.1 of the License, or (at your option) any later version.
  *
  * This library is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  * Lesser General Public License for more details.
  *
  * You should have received a copy of the GNU Lesser General Public
  * License along with this library; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
  *
  */
 
 #include "indexcleaner.h"
 #include "fileindexerconfig.h"
 
 #include "database.h"
 #include "transaction.h"
 #include "idutils.h"
 
 #include "baloodebug.h"
 
 #include <QFile>
 #include <QMimeDatabase>
 
 using namespace Baloo;
 
 IndexCleaner::IndexCleaner(Database* db, FileIndexerConfig* config)
     : m_db(db)
     , m_config(config)
 {
     Q_ASSERT(db);
     Q_ASSERT(config);
 }
 
 void IndexCleaner::run()
 {
     QMimeDatabase mimeDb;
 
     Transaction tr(m_db, Transaction::ReadWrite);
 
     auto shouldDelete = [&](quint64 id) {
         if (!id) {
             return false;
         }
 
         QString url = tr.documentUrl(id);
 
         if (!QFile::exists(url)) {
             qCDebug(BALOO) << "not exists: " << url;
             return true;
         }
 
         if (!m_config->shouldBeIndexed(url)) {
             qCDebug(BALOO) << "should not be indexed: " << url;
             return true;
         }
 
         // FIXME: This mimetype is not completely accurate!
         QString mimetype = mimeDb.mimeTypeForFile(url, QMimeDatabase::MatchExtension).name();
         if (!m_config->shouldMimeTypeBeIndexed(mimetype)) {
             qCDebug(BALOO) << "mimetype should not be indexed: " << url << mimetype;
             return true;
         }
 
         return false;
     };
 
     const auto includeFolders = m_config->includeFolders();
     for (const QString& folder : includeFolders) {
         quint64 id = filePathToId(QFile::encodeName(folder));
-        tr.removeRecursively(id, shouldDelete);
+        if (id > 0) {
+            tr.removeRecursively(id, shouldDelete);
+        }
     }
     const auto excludeFolders = m_config->excludeFolders();
     for (const QString& folder : excludeFolders) {
         quint64 id = filePathToId(QFile::encodeName(folder));
-        if (tr.hasDocument(id)) {
+        if (id > 0 && tr.hasDocument(id)) {
             tr.removeRecursively(id, shouldDelete);
         }
     }
     tr.commit();
 
     Q_EMIT done();
 }