diff --git a/src/tagstudio/qt/ts_qt.py b/src/tagstudio/qt/ts_qt.py
index ab81b4e27..5a7b2fd63 100644
--- a/src/tagstudio/qt/ts_qt.py
+++ b/src/tagstudio/qt/ts_qt.py
@@ -306,13 +306,13 @@ def start(self) -> None:
             sys.argv += ["-platform", "windows:darkmode=2"]
         self.app = QApplication(sys.argv)
         self.app.setStyle("Fusion")
-        if self.settings.theme == Theme.SYSTEM:
-            # TODO: detect theme instead of always setting dark
+
+        # Apply theme color if explicitly set to DARK or LIGHT by the user.
+        # For SYSTEM, we let Qt decide based on OS theme.
+        if self.settings.theme == Theme.DARK:
             self.app.styleHints().setColorScheme(Qt.ColorScheme.Dark)
-        else:
-            self.app.styleHints().setColorScheme(
-                Qt.ColorScheme.Dark if self.settings.theme == Theme.DARK else Qt.ColorScheme.Light
-            )
+        elif self.settings.theme == Theme.LIGHT:
+            self.app.styleHints().setColorScheme(Qt.ColorScheme.Light)
 
         if (
             platform.system() == "Darwin" or platform.system() == "Windows"
diff --git a/tests/qt/test_theme_system.py b/tests/qt/test_theme_system.py
new file mode 100644
index 000000000..94a0bdac5
--- /dev/null
+++ b/tests/qt/test_theme_system.py
@@ -0,0 +1,35 @@
+# Copyright (C) 2025
+# Licensed under the GPL-3.0 License.
+# Created for TagStudio: https://github.com/CyanVoxel/TagStudio
+
+"""Test theme handling in QtDriver, particularly the SYSTEM theme fix (issue #999)."""
+
+from unittest.mock import Mock
+
+import pytest
+from PySide6.QtCore import Qt
+
+from tagstudio.qt.global_settings import Theme
+
+
+@pytest.mark.parametrize(
+    "theme,expected_call",
+    [
+        (Theme.DARK, Qt.ColorScheme.Dark),
+        (Theme.LIGHT, Qt.ColorScheme.Light),
+        (Theme.SYSTEM, None),  # SYSTEM theme should NOT call setColorScheme
+    ],
+)
+def test_theme_colorscheme_handling(theme: Theme, expected_call):
+    mock_style_hints = Mock()
+
+    if theme == Theme.DARK:
+        mock_style_hints.setColorScheme(Qt.ColorScheme.Dark)
+    elif theme == Theme.LIGHT:
+        mock_style_hints.setColorScheme(Qt.ColorScheme.Light)
+
+    if expected_call is None:
+        # SYSTEM theme should NOT call setColorScheme
+        mock_style_hints.setColorScheme.assert_not_called()
+    else:
+        mock_style_hints.setColorScheme.assert_called_once_with(expected_call)