diff --git a/CMakeLists.txt b/CMakeLists.txt
index 77122499e..168dd6507 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -21,6 +21,7 @@
 # Variables:
 #   BUILD_WITH_QT6 - Build either with Qt 6 or Qt 5.
 #   NO_UPDATE_CHECK - Disable automatic checking for new application updates.
+#   IS_FLATPAK_BUILD - Set to "ON" when building RSS Guard with Flatpak.
 #   USE_WEBENGINE - if specified, then QtWebEngine module for internal web browser is used.
 #                   Otherwise simple text component is used and some features will be disabled.
 #                   Default value is "false". If QtWebEngine is installed during compilation, then
@@ -108,6 +109,7 @@ option(UPDATE_TRANSLATIONS "Call lupdate to update translation files from source
 option(FORCE_COLORED_OUTPUT "Always produce ANSI-colored output (GCC/Clang only)" OFF)
 option(REVISION_FROM_GIT "Get revision using `git rev-parse`" ON)
 option(NO_UPDATE_CHECK "Disable automatic checking for new application updates" OFF)
+option(IS_FLATPAK_BUILD "Set to 'ON' when building RSS Guard with Flatpak." OFF)
 
 # Import Qt libraries.
 set(QT6_MIN_VERSION 6.3.0)
@@ -197,6 +199,7 @@ add_compile_definitions(
   APP_URL="${APP_URL}"
   APP_LONG_NAME="${APP_NAME} ${CMAKE_PROJECT_VERSION}"
   APP_LOW_NAME="${CMAKE_PROJECT_NAME}"
+  APP_REVERSE_NAME="com.github.${CMAKE_PROJECT_NAME}"
 
   QT_USE_QSTRINGBUILDER
   QT_USE_FAST_CONCATENATION
@@ -209,6 +212,10 @@ if(NO_UPDATE_CHECK)
   add_compile_definitions(NO_UPDATE_CHECK)
 endif()
 
+if(IS_FLATPAK_BUILD)
+  add_compile_definitions(IS_FLATPAK_BUILD)
+endif()
+
 # Configure and copy some needed files.
 if(WIN32)
   configure_file(
diff --git a/resources/desktop/com.github.rssguard.desktop.autostart b/resources/desktop/com.github.rssguard.desktop.autostart
index a7008da48..3979067ae 100644
--- a/resources/desktop/com.github.rssguard.desktop.autostart
+++ b/resources/desktop/com.github.rssguard.desktop.autostart
@@ -3,8 +3,8 @@ Version=1.0
 Type=Application
 Terminal=false
 Name=RSS Guard
-TryExec=rssguard
-Exec=rssguard
+TryExec=%1
+Exec=%1
 Hidden=false
 X-GNOME-Autostart-Delay=15
 X-LXQt-Need-Tray=true
\ No newline at end of file
diff --git a/src/librssguard/miscellaneous/systemfactory.cpp b/src/librssguard/miscellaneous/systemfactory.cpp
index 5b8f4debe..bd7a65928 100644
--- a/src/librssguard/miscellaneous/systemfactory.cpp
+++ b/src/librssguard/miscellaneous/systemfactory.cpp
@@ -6,6 +6,7 @@
 #include "gui/dialogs/formupdate.h"
 #include "miscellaneous/application.h"
 #include "miscellaneous/systemfactory.h"
+#include "exceptions/applicationexception.h"
 #include "network-web/networkfactory.h"
 
 #if defined(Q_OS_WIN)
@@ -157,7 +158,22 @@ bool SystemFactory::setAutoStartStatus(AutoStartStatus new_status) {
       const QString source_autostart_desktop_file =
         QString(APP_DESKTOP_ENTRY_PATH) + QDir::separator() + APP_DESKTOP_SOURCE_ENTRY_FILE;
 
-      return QFile::copy(source_autostart_desktop_file, destination_file);
+      try {
+      QString desktop_file_contents = QString::fromUtf8(IOFactory::readFile(source_autostart_desktop_file));
+
+#if defined(IS_FLATPAK_BUILD)
+      desktop_file_contents = desktop_file_contents.arg(QSL("flatpak run %1").arg(QSL(APP_REVERSE_NAME)));
+#else
+      desktop_file_contents = desktop_file_contents.arg(QSL(APP_LOW_NAME));
+#endif
+
+        IOFactory::writeFile(destination_file, desktop_file_contents.toUtf8());
+      }
+      catch (const ApplicationException& ex) {
+        return false;
+      }
+
+      return true;
     }
 
     case AutoStartStatus::Disabled: