diff --git a/docs/release_notes/next/fix-2209-theme_os_startup_instability b/docs/release_notes/next/fix-2209-theme_os_startup_instability
new file mode 100644
index 00000000000..413bb9cb896
--- /dev/null
+++ b/docs/release_notes/next/fix-2209-theme_os_startup_instability
@@ -0,0 +1 @@
+#2209: Mantid Imaging now switches between Fusion and qt-material themes correctly
\ No newline at end of file
diff --git a/mantidimaging/gui/windows/main/presenter.py b/mantidimaging/gui/windows/main/presenter.py
index 40bee214c68..7c65df284fc 100644
--- a/mantidimaging/gui/windows/main/presenter.py
+++ b/mantidimaging/gui/windows/main/presenter.py
@@ -853,28 +853,24 @@ def do_update_UI(self) -> None:
             override_os_theme = settings.value('override_os_theme')
         os_theme = settings.value('os_theme')
         font = QFont(settings.value('default_font_family'), int(extra_style['font_size'].replace('px', '')))
-        for window in [
-                self.view, self.view.recon, self.view.live_viewer, self.view.spectrum_viewer, self.view.filters,
-                self.view.settings_window
-        ]:
-            if window:
-                QApplication.instance().setFont(font)
-                window.setStyleSheet(theme)
-                if theme == 'Fusion':
-                    if override_os_theme == 'False':
-                        if os_theme == 'Light':
-                            self.use_fusion_light_mode()
-                        elif os_theme == 'Dark':
-                            self.use_fusion_dark_mode()
-                    else:
-                        if use_dark_mode == 'True':
-                            self.use_fusion_dark_mode()
-                        else:
-                            self.use_fusion_light_mode()
-                    QApplication.instance().setFont(font)
-                    window.setStyleSheet(theme)
+        app = QApplication.instance()
+
+        app.setFont(font)
+        if theme == 'Fusion':
+            if override_os_theme == 'False':
+                if os_theme == 'Light':
+                    self.use_fusion_light_mode()
+                elif os_theme == 'Dark':
+                    self.use_fusion_dark_mode()
+            else:
+                if use_dark_mode == 'True':
+                    self.use_fusion_dark_mode()
                 else:
-                    apply_stylesheet(window, theme=theme, invert_secondary=False, extra=extra_style)
+                    self.use_fusion_light_mode()
+            app.setStyle(theme)
+            app.setStyleSheet('')
+        else:
+            apply_stylesheet(app, theme=theme, invert_secondary=False, extra=extra_style)
 
     @staticmethod
     def use_fusion_dark_mode() -> None: