diff --git a/autotests/unit/file/filewatchtest.cpp b/autotests/unit/file/filewatchtest.cpp
--- a/autotests/unit/file/filewatchtest.cpp
+++ b/autotests/unit/file/filewatchtest.cpp
@@ -43,7 +43,7 @@
         m_tempDir = new QTemporaryDir();
         m_db = new Database(m_tempDir->path());
         m_db->open(Database::CreateDatabase);
-        m_dbusInterface = new MainHub(m_db, &m_config);
+        m_dbusInterface = new MainHub(m_db, &m_config, false);
     }
 
     void testFileCreation();
diff --git a/src/file/fileindexerconfig.h b/src/file/fileindexerconfig.h
--- a/src/file/fileindexerconfig.h
+++ b/src/file/fileindexerconfig.h
@@ -69,12 +69,6 @@
 
     bool onlyBasicIndexing() const;
 
-    /**
-     * \return \c true if the service is run for the first time 
-     * (or after manually setting "first run=true" in the config).
-     */
-    bool isInitialRun() const;
-
     /**
     * Check if \p folder can be searched.
     * \p folder can be searched if itself or one of its descendants is indexed.
@@ -166,12 +160,6 @@
      */
     void forceConfigUpdate();
 
-    /**
-     * Should be called once the initial indexing is done, ie. all folders
-     * have been indexed.
-     */
-    void setInitialRun(bool isInitialRun);
-
 private:
 
     void buildFolderCache();
diff --git a/src/file/fileindexerconfig.cpp b/src/file/fileindexerconfig.cpp
--- a/src/file/fileindexerconfig.cpp
+++ b/src/file/fileindexerconfig.cpp
@@ -26,7 +26,6 @@
 #include <QDir>
 
 #include <QStandardPaths>
-#include <KConfigGroup>
 #include "baloosettings.h"
 
 namespace
@@ -142,13 +141,6 @@
     return m_onlyBasicIndexing;
 }
 
-bool FileIndexerConfig::isInitialRun() const
-{
-    KConfig config(QStringLiteral("baloofilerc"));
-    return config.group("General").readEntry("first run", true);
-}
-
-
 bool FileIndexerConfig::canBeSearched(const QString& folder) const
 {
     QFileInfo fi(folder);
@@ -370,14 +362,6 @@
     m_onlyBasicIndexing = m_settings->onlyBasicIndexing();
 }
 
-void FileIndexerConfig::setInitialRun(bool isInitialRun)
-{
-    // Don't use kcfg, it will break KCM default state
-    KConfig config(QStringLiteral("baloofilerc"));
-    config.group("General").writeEntry("first run", isInitialRun);
-    config.sync();
-}
-
 int FileIndexerConfig::databaseVersion() const
 {
     return m_settings->dbVersion();
diff --git a/src/file/fileindexscheduler.h b/src/file/fileindexscheduler.h
--- a/src/file/fileindexscheduler.h
+++ b/src/file/fileindexscheduler.h
@@ -43,7 +43,7 @@
 
     Q_PROPERTY(int state READ state NOTIFY stateChanged)
 public:
-    FileIndexScheduler(Database* db, FileIndexerConfig* config, QObject* parent = nullptr);
+    FileIndexScheduler(Database* db, FileIndexerConfig* config, bool firstRun, QObject* parent = nullptr);
     ~FileIndexScheduler() override;
     int state() const { return m_indexerState; }
 
@@ -89,6 +89,7 @@
     void scheduleIndexing();
     void scheduleCheckUnindexedFiles();
     void scheduleCheckStaleIndexEntries();
+    void startupFinished();
 
     Q_SCRIPTABLE void suspend() { setSuspend(true); }
     Q_SCRIPTABLE void resume() { setSuspend(false); }
@@ -105,6 +106,7 @@
     bool isIndexerIdle() {
         return m_isGoingIdle ||
                (m_indexerState == Suspended) ||
+               (m_indexerState == Startup) ||
                (m_indexerState == Idle) ||
                (m_indexerState == LowPowerIdle);
     }
@@ -130,6 +132,8 @@
     bool m_checkStaleIndexEntries;
     bool m_isGoingIdle;
     bool m_isSuspended;
+    bool m_isFirstRun;
+    bool m_inStartup;
 };
 
 }
diff --git a/src/file/fileindexscheduler.cpp b/src/file/fileindexscheduler.cpp
--- a/src/file/fileindexscheduler.cpp
+++ b/src/file/fileindexscheduler.cpp
@@ -37,18 +37,20 @@
 
 using namespace Baloo;
 
-FileIndexScheduler::FileIndexScheduler(Database* db, FileIndexerConfig* config, QObject* parent)
+FileIndexScheduler::FileIndexScheduler(Database* db, FileIndexerConfig* config, bool firstRun, QObject* parent)
     : QObject(parent)
     , m_db(db)
     , m_config(config)
     , m_provider(db)
     , m_contentIndexer(nullptr)
-    , m_indexerState(Idle)
+    , m_indexerState(Startup)
     , m_timeEstimator(config, this)
     , m_checkUnindexedFiles(false)
     , m_checkStaleIndexEntries(false)
     , m_isGoingIdle(false)
     , m_isSuspended(false)
+    , m_isFirstRun(firstRun)
+    , m_inStartup(true)
 {
     Q_ASSERT(db);
     Q_ASSERT(config);
@@ -79,6 +81,11 @@
     m_threadPool.waitForDone(0); // wait 0 msecs
 }
 
+void FileIndexScheduler::startupFinished() {
+    m_inStartup = false;
+    QTimer::singleShot(0, this, &FileIndexScheduler::scheduleIndexing);
+}
+
 void FileIndexScheduler::scheduleIndexing()
 {
     if (!isIndexerIdle()) {
@@ -94,7 +101,12 @@
         return;
     }
 
-    if (m_config->isInitialRun()) {
+    if (m_isFirstRun) {
+        if (m_inStartup) {
+            return;
+        }
+
+        m_isFirstRun = false;
         auto runnable = new FirstRunIndexer(m_db, m_config, m_config->includeFolders());
         connect(runnable, &FirstRunIndexer::done, this, &FileIndexScheduler::runnerFinished);
 
@@ -146,6 +158,14 @@
         return;
     }
 
+    if (m_inStartup) {
+        if (m_indexerState != Startup) {
+            m_indexerState = Startup;
+            Q_EMIT stateChanged(m_indexerState);
+        }
+        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) {
diff --git a/src/file/firstrunindexer.cpp b/src/file/firstrunindexer.cpp
--- a/src/file/firstrunindexer.cpp
+++ b/src/file/firstrunindexer.cpp
@@ -41,12 +41,6 @@
 
 void FirstRunIndexer::run()
 {
-    Q_ASSERT(m_config->isInitialRun());
-    {
-        Transaction tr(m_db, Transaction::ReadOnly);
-        Q_ASSERT_X(tr.size() == 0, "FirstRunIndexer", "The database is not empty on first run");
-    }
-
     QMimeDatabase mimeDb;
     BasicIndexingJob::IndexingLevel level = m_config->onlyBasicIndexing() ? BasicIndexingJob::NoLevel
         : BasicIndexingJob::MarkForContentIndexing;
@@ -87,7 +81,5 @@
         tr.commit();
     }
 
-    m_config->setInitialRun(false);
-
     Q_EMIT done();
 }
diff --git a/src/file/indexerstate.h b/src/file/indexerstate.h
--- a/src/file/indexerstate.h
+++ b/src/file/indexerstate.h
@@ -38,6 +38,7 @@
         StaleIndexEntriesClean,
         LowPowerIdle,
         Unavailable,
+        Startup,
 };
 
 inline QString stateString(IndexerState state)
@@ -77,6 +78,9 @@
     case Unavailable:
         status = i18n("Not Running");
         break;
+    case Startup:
+        status = i18n("Starting");
+        break;
     }
     return status;
 }
diff --git a/src/file/main.cpp b/src/file/main.cpp
--- a/src/file/main.cpp
+++ b/src/file/main.cpp
@@ -72,9 +72,7 @@
         migrator.migrate();
     }
 
-    if (!QFile::exists(path + "/index")) {
-        indexerConfig.setInitialRun(true);
-    }
+    bool firstRun = !QFile::exists(path + "/index");
 
     // HACK: Until we start using lmdb with robust mutex support. We're just going to remove
     //       the lock manually in the baloo_file process.
@@ -90,15 +88,15 @@
         qWarning() << "Failed to create database, removing corrupted database.";
         QFile::remove(path + "/index");
         QFile::remove(path + "/index-lock");
-        indexerConfig.setInitialRun(true);
+        firstRun = true;
 
         // try to create now after cleanup, if still no works => fail
         if (!db->open(Baloo::Database::CreateDatabase)) {
             qWarning() << "Failed to create database after deleting corrupted one.";
             return 1;
         }
     }
 
-    Baloo::MainHub hub(db, &indexerConfig);
+    Baloo::MainHub hub(db, &indexerConfig, firstRun);
     return app.exec();
 }
diff --git a/src/file/mainhub.h b/src/file/mainhub.h
--- a/src/file/mainhub.h
+++ b/src/file/mainhub.h
@@ -36,7 +36,7 @@
     Q_OBJECT
     Q_CLASSINFO("D-Bus Interface", "org.kde.baloo.main")
 public:
-    MainHub(Database* db, FileIndexerConfig* config);
+    MainHub(Database* db, FileIndexerConfig* config, bool firstRun);
 
 public Q_SLOTS:
     Q_SCRIPTABLE void quit() const;
diff --git a/src/file/mainhub.cpp b/src/file/mainhub.cpp
--- a/src/file/mainhub.cpp
+++ b/src/file/mainhub.cpp
@@ -27,11 +27,11 @@
 
 using namespace Baloo;
 
-MainHub::MainHub(Database* db, FileIndexerConfig* config)
+MainHub::MainHub(Database* db, FileIndexerConfig* config, bool firstRun)
     : m_db(db)
     , m_config(config)
     , m_fileWatcher(db, config, this)
-    , m_fileIndexScheduler(db, config, this)
+    , m_fileIndexScheduler(db, config, firstRun, this)
 {
     Q_ASSERT(db);
     Q_ASSERT(config);
@@ -50,11 +50,16 @@
     bus.registerObject(QStringLiteral("/"), this, QDBusConnection::ExportAllSlots |
                         QDBusConnection::ExportScriptableSignals | QDBusConnection::ExportAdaptors);
 
-    if (!m_config->isInitialRun()) {
+    if (firstRun) {
+        QTimer::singleShot(5000, this, [this] {
+            m_fileIndexScheduler.startupFinished();
+        });
+    } else {
         // Delay these checks so we don't end up consuming excessive resources on login
         QTimer::singleShot(5000, this, [this] {
             m_fileIndexScheduler.checkUnindexedFiles();
             m_fileIndexScheduler.checkStaleIndexEntries();
+            m_fileIndexScheduler.startupFinished();
         });
     }
     QTimer::singleShot(0, &m_fileWatcher, &FileWatch::watchIndexedFolders);
diff --git a/src/file/migrator.cpp b/src/file/migrator.cpp
--- a/src/file/migrator.cpp
+++ b/src/file/migrator.cpp
@@ -60,5 +60,4 @@
     }
 
     m_config->setDatabaseVersion(s_dbVersion);
-    m_config->setInitialRun(true);
 }
diff --git a/src/lib/CMakeLists.txt b/src/lib/CMakeLists.txt
--- a/src/lib/CMakeLists.txt
+++ b/src/lib/CMakeLists.txt
@@ -68,7 +68,7 @@
     GROUP_BASE_NAME KF
     VERSION ${KF5_VERSION}
     DEPRECATED_BASE_VERSION 0
-    DEPRECATION_VERSIONS 5.55
+    DEPRECATION_VERSIONS 5.55 5.69
     EXCLUDE_DEPRECATED_BEFORE_AND_AT ${EXCLUDE_DEPRECATED_BEFORE_AND_AT}
 )
 
diff --git a/src/lib/indexerconfig.h b/src/lib/indexerconfig.h
--- a/src/lib/indexerconfig.h
+++ b/src/lib/indexerconfig.h
@@ -87,12 +87,21 @@
     void setExcludeFilters(const QStringList& excludeFilters);
     void setExcludeMimetypes(const QStringList& excludeMimetypes);
 
+#if BALOO_CORE_BUILD_DEPRECATED_SINCE(5, 69)
     /**
-     * \return \c true if the service is run for the first time 
-     * (or after manually setting "first run=true" in the config).
+     * @deprecated Since 5.69. Do not use this function, firstRun is no longer
+     * exposed in the config, as it is an internal baloo state.
+     * \return \c false
      */
+    BALOO_CORE_DEPRECATED_VERSION(5, 69, "Do not use. firstRun is a baloo internal state")
     bool firstRun() const;
+    /**
+     * @deprecated Since 5.69. Do not use this function. Since 5.69, calling
+     * it no longer has any effect.
+     */
+    BALOO_CORE_DEPRECATED_VERSION(5, 69, "Do not use. firstRun is a baloo internal state")
     void setFirstRun(bool firstRun) const;
+#endif
 
     bool indexHidden() const;
     void setIndexHidden(bool value) const;
diff --git a/src/lib/indexerconfig.cpp b/src/lib/indexerconfig.cpp
--- a/src/lib/indexerconfig.cpp
+++ b/src/lib/indexerconfig.cpp
@@ -109,15 +109,16 @@
     d->m_settings.setExcludedMimetypes(excludeMimetypes);
 }
 
+#if BALOO_CORE_BUILD_DEPRECATED_SINCE(5, 69)
 bool IndexerConfig::firstRun() const
 {
-    return d->m_config.isInitialRun();
+    return false;
 }
 
-void IndexerConfig::setFirstRun(bool firstRun) const
+void IndexerConfig::setFirstRun(bool) const
 {
-    d->m_config.setInitialRun(firstRun);
 }
+#endif
 
 bool IndexerConfig::indexHidden() const
 {