diff --git a/src/engine/transaction.h b/src/engine/transaction.h
--- a/src/engine/transaction.h
+++ b/src/engine/transaction.h
@@ -113,6 +113,7 @@
         m_writeTrans->removeRecursively(id, shouldDelete);
     }
 
+    void pruneFsTree();
     void replaceDocument(const Document& doc, DocumentOperations operations);
     void setPhaseOne(quint64 id);
     void removePhaseOne(quint64 id);
diff --git a/src/engine/transaction.cpp b/src/engine/transaction.cpp
--- a/src/engine/transaction.cpp
+++ b/src/engine/transaction.cpp
@@ -254,6 +254,21 @@
     m_writeTrans->replaceDocument(doc, operations);
 }
 
+void Transaction::pruneFsTree()
+{
+    DocumentUrlDB docUrlDb(m_dbis.idTreeDbi, m_dbis.idFilenameDbi, m_txn);
+    auto map = docUrlDb.toTestMap();
+
+    QTextStream out(stdout);
+    for (quint64 id: map.keys()) {
+        QByteArray url = docUrlDb.get(id);
+        if (!QFileInfo::exists(url)) {
+            removeDocument(id);
+            out << "Purged " << id << " " << url << endl;
+        }
+    }
+}
+
 void Transaction::commit()
 {
     Q_ASSERT(m_txn);
diff --git a/src/tools/balooctl/main.cpp b/src/tools/balooctl/main.cpp
--- a/src/tools/balooctl/main.cpp
+++ b/src/tools/balooctl/main.cpp
@@ -87,6 +87,7 @@
     parser.addPositionalArgument(QStringLiteral("clear"), i18n("Forget the specified files"));
     parser.addPositionalArgument(QStringLiteral("config"), i18n("Modify the Baloo configuration"));
     parser.addPositionalArgument(QStringLiteral("monitor"), i18n("Monitor the file indexer"));
+    parser.addPositionalArgument(QStringLiteral("clean"), i18n("Remove unresolvable file paths from the index"));
     parser.addPositionalArgument(QStringLiteral("indexSize"), i18n("Display the disk space used by index"));
     parser.addOption(QCommandLineOption(QStringList() << QStringLiteral("f") << QStringLiteral("format"), 
         i18n("Output format <%1|%2|%3>.\nOnly applies to \"%4\"", 
@@ -322,6 +323,19 @@
         return mon.exec(parser);
     }
 
+    if (command == QStringLiteral("clean")) {
+        Database *db = globalDatabaseInstance();
+        if (!db->open(Database::ReadWriteDatabase)) {
+            err << "Baloo Index could not be opened\n";
+            return 1;
+        }
+
+        Transaction tr(db, Transaction::ReadWrite);
+        tr.pruneFsTree();
+        tr.commit();
+        return 0;
+    }
+
     /*
      TODO: Make separate executable
      if (command == QStringLiteral("checkDb")) {