diff --git a/src/file/fileindexscheduler.h b/src/file/fileindexscheduler.h
--- a/src/file/fileindexscheduler.h
+++ b/src/file/fileindexscheduler.h
@@ -85,6 +85,7 @@
 
     void handleFileRemoved(const QString& file);
 
+    void updateConfig();
     void scheduleIndexing();
     void scheduleCheckUnindexedFiles();
     void scheduleCheckStaleIndexEntries();
diff --git a/src/file/fileindexscheduler.cpp b/src/file/fileindexscheduler.cpp
--- a/src/file/fileindexscheduler.cpp
+++ b/src/file/fileindexscheduler.cpp
@@ -124,6 +124,19 @@
         return;
     }
 
+    // This has to 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::runnerFinished);
+
+        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;
@@ -142,16 +155,6 @@
         return;
     }
 
-    if (m_checkStaleIndexEntries) {
-        auto runnable = new IndexCleaner(m_db, m_config);
-        connect(runnable, &IndexCleaner::done, this, &FileIndexScheduler::runnerFinished);
-
-        m_threadPool.start(runnable);
-        m_checkStaleIndexEntries = false;
-        m_indexerState = StaleIndexEntriesClean;
-        Q_EMIT stateChanged(m_indexerState);
-        return;
-    }
     m_indexerState = Idle;
     Q_EMIT stateChanged(m_indexerState);
 }
@@ -165,6 +168,31 @@
     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()
+{
+    // Interrupt content indexer, to avoid indexing files that should
+    // not be indexed (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);
+    m_checkStaleIndexEntries = true;
+    m_checkUnindexedFiles = true;
+    scheduleIndexing();
+}
+
 void FileIndexScheduler::handleFileRemoved(const QString& file)
 {
     if (!file.endsWith(QLatin1Char('/'))) {
diff --git a/src/file/indexcleaner.cpp b/src/file/indexcleaner.cpp
--- a/src/file/indexcleaner.cpp
+++ b/src/file/indexcleaner.cpp
@@ -76,6 +76,13 @@
         quint64 id = filePathToId(QFile::encodeName(folder));
         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)) {
+            tr.removeRecursively(id);
+        }
+    }
     tr.commit();
 
     Q_EMIT done();
diff --git a/src/file/mainhub.cpp b/src/file/mainhub.cpp
--- a/src/file/mainhub.cpp
+++ b/src/file/mainhub.cpp
@@ -65,9 +65,8 @@
 void MainHub::updateConfig()
 {
     m_config->forceConfigUpdate();
-    // FIXME!!
-    //m_fileIndexer.updateConfig();
     m_fileWatcher.updateIndexedFoldersWatches();
+    m_fileIndexScheduler.updateConfig();
 }
 
 void MainHub::registerBalooWatcher(const QString &service)