Index: src/file/fileindexscheduler.h
===================================================================
--- src/file/fileindexscheduler.h
+++ src/file/fileindexscheduler.h
@@ -74,6 +74,7 @@
 
     void handleFileRemoved(const QString& file);
 
+    void updateConfig();
     void scheduleIndexing();
     void scheduleCheckUnindexedFiles();
     void scheduleCheckStaleIndexEntries();
Index: src/file/fileindexscheduler.cpp
===================================================================
--- src/file/fileindexscheduler.cpp
+++ src/file/fileindexscheduler.cpp
@@ -122,6 +122,19 @@
         return;
     }
 
+    // This should be above content indexing, because there can be files that should not be indexed in the DB
+    // (i.e. if config was changed)
+    if (m_checkStaleIndexEntries) {
+        auto runnable = new IndexCleaner(m_db, m_config);
+        connect(runnable, &IndexCleaner::done, this, &FileIndexScheduler::scheduleIndexing);
+
+        m_threadPool.start(runnable);
+        m_checkStaleIndexEntries = false;
+        m_indexerState = StaleIndexEntriesClean;
+        Q_EMIT stateChanged(m_indexerState);
+        return;
+    }
+
     if (m_provider.size() && !m_powerMonitor.isOnBattery()) {
         m_threadPool.start(m_contentIndexer);
         m_indexerState = ContentIndexing;
@@ -140,16 +153,6 @@
         return;
     }
 
-    if (m_checkStaleIndexEntries) {
-        auto runnable = new IndexCleaner(m_db, m_config);
-        connect(runnable, &IndexCleaner::done, this, &FileIndexScheduler::scheduleIndexing);
-
-        m_threadPool.start(runnable);
-        m_checkStaleIndexEntries = false;
-        m_indexerState = StaleIndexEntriesClean;
-        Q_EMIT stateChanged(m_indexerState);
-        return;
-    }
     m_indexerState = Idle;
     Q_EMIT stateChanged(m_indexerState);
 }
@@ -163,6 +166,30 @@
     list.erase(tail, list.end());
 }
 
+static void removeShouldNotIndex(QStringList& list, FileIndexerConfig* config)
+{
+    const auto tail = std::remove_if(list.begin(), list.end(),
+        [config](const QString& file) {
+            return !config->shouldBeIndexed(file);
+        });
+    list.erase(tail, list.end());
+}
+
+void FileIndexScheduler::updateConfig()
+{
+    // Rescheduling content indexer
+    // (so we won't keep indexing files that should not be, bug 373430)
+    if (m_indexerState == ContentIndexing) {
+        m_contentIndexer->quit();
+        m_indexerState = Idle;
+    }
+    removeShouldNotIndex(m_newFiles, m_config);
+    removeShouldNotIndex(m_modifiedFiles, m_config);
+    removeShouldNotIndex(m_xattrFiles, m_config);
+    checkStaleIndexEntries();
+    checkUnindexedFiles();
+}
+
 void FileIndexScheduler::handleFileRemoved(const QString& file)
 {
     if (!file.endsWith(QLatin1Char('/'))) {
Index: src/file/indexcleaner.cpp
===================================================================
--- src/file/indexcleaner.cpp
+++ src/file/indexcleaner.cpp
@@ -70,12 +70,7 @@
 
         return false;
     };
-
-    const auto includeFolders = m_config->includeFolders();
-    for (const QString& folder : includeFolders) {
-        quint64 id = filePathToId(QFile::encodeName(folder));
-        tr.removeRecursively(id, shouldDelete);
-    }
+    tr.removeRecursively(0, shouldDelete);
     tr.commit();
 
     Q_EMIT done();
Index: src/file/mainhub.cpp
===================================================================
--- src/file/mainhub.cpp
+++ src/file/mainhub.cpp
@@ -66,9 +66,8 @@
 void MainHub::updateConfig()
 {
     m_config->forceConfigUpdate();
-    // FIXME!!
-    //m_fileIndexer.updateConfig();
     m_fileWatcher.updateIndexedFoldersWatches();
+    m_fileIndexScheduler.updateConfig();
 }
 
 void MainHub::registerBalooWatcher(const QString &service)