diff --git a/docs/theme-import.md b/docs/theme-import.md
index 25d25e83..2097fcad 100644
--- a/docs/theme-import.md
+++ b/docs/theme-import.md
@@ -43,6 +43,20 @@ Hex strings as in VS Code: `#RRGGBB`, `#RRGGBBAA`, `#RGB`, `#RGBA` (see
 
 Comments and trailing commas are stripped before parse (`stripJsonc`).
 
+## User overrides (#45)
+
+User customizations are stored as VS Code keys → hex strings in
+`theme_overrides_json` (`AppSettings`). Merge order:
+
+```
+effectiveColors = merge(importedTheme.colors, userOverrides)
+```
+
+Built-in preset defaults apply for keys not present in the merged map.
+
+API: `ThemeController.setWorkbenchColor(key, color?)`,
+`ThemeController.clearColorOverrides()` (user layer only).
+
 ## Fixtures (tests)
 
 - `test/fixtures/themes/dark_subset.json`
diff --git a/lib/core/storage/app_settings.dart b/lib/core/storage/app_settings.dart
index 8ff1c188..660ab4f3 100644
--- a/lib/core/storage/app_settings.dart
+++ b/lib/core/storage/app_settings.dart
@@ -1,3 +1,5 @@
+import 'dart:convert';
+
 import 'package:shadcn_flutter/shadcn_flutter.dart';
 
 import '../theme/querya_theme_preset.dart';
@@ -50,6 +52,7 @@ abstract final class AppSettingsKeys {
   static const sqlHistoryMaxEntries = 'sql_history_max_entries';
   static const themeMode = 'theme_mode';
   static const themePreset = 'theme_preset';
+  static const themeOverridesJson = 'theme_overrides_json';
 }
 
 /// Bumps [listenable] when any preference is persisted so open screens can reload.
@@ -211,9 +214,51 @@ class AppSettings {
     AppSettingsRevision.bump();
   }
 
+  Future<Map<String, String>> getThemeColorOverrides() async {
+    final v =
+        await LocalDb.instance.getAppSetting(AppSettingsKeys.themeOverridesJson);
+    if (v == null || v.isEmpty) return {};
+    try {
+      final decoded = jsonDecode(v);
+      if (decoded is! Map) return {};
+      final out = <String, String>{};
+      for (final entry in decoded.entries) {
+        final key = entry.key?.toString();
+        final value = entry.value?.toString();
+        if (key != null &&
+            key.isNotEmpty &&
+            value != null &&
+            value.isNotEmpty) {
+          out[key] = value;
+        }
+      }
+      return out;
+    } on FormatException {
+      return {};
+    }
+  }
+
+  Future<void> setThemeColorOverrides(Map<String, String> overrides) async {
+    if (overrides.isEmpty) {
+      await clearThemeColorOverrides();
+      return;
+    }
+    await LocalDb.instance.setAppSetting(
+      AppSettingsKeys.themeOverridesJson,
+      jsonEncode(overrides),
+    );
+    AppSettingsRevision.bump();
+  }
+
+  Future<void> clearThemeColorOverrides() async {
+    await LocalDb.instance.deleteAppSetting(AppSettingsKeys.themeOverridesJson);
+    AppSettingsRevision.bump();
+  }
+
   Future<void> clearThemeSettings() async {
     await LocalDb.instance.deleteAppSetting(AppSettingsKeys.themeMode);
     await LocalDb.instance.deleteAppSetting(AppSettingsKeys.themePreset);
+    await LocalDb.instance.deleteAppSetting(AppSettingsKeys.themeOverridesJson);
     AppSettingsRevision.bump();
   }
 }
diff --git a/lib/core/theme/parser/color_parser.dart b/lib/core/theme/parser/color_parser.dart
index c4cae9f8..b1c7cdc4 100644
--- a/lib/core/theme/parser/color_parser.dart
+++ b/lib/core/theme/parser/color_parser.dart
@@ -33,6 +33,20 @@ Color parseVsCodeColor(String input) {
   throw FormatException('Unsupported color format: $input');
 }
 
+/// Encodes a [Color] as a VS Code hex string (`#RRGGBB` or `#RRGGBBAA`).
+String formatVsCodeColor(Color color) {
+  String channel(double component) =>
+      (component * 255.0).round().clamp(0, 255).toRadixString(16).padLeft(2, '0');
+  final rr = channel(color.r);
+  final gg = channel(color.g);
+  final bb = channel(color.b);
+  if (color.a < 1.0) {
+    final aa = channel(color.a);
+    return '#$rr$gg$bb$aa';
+  }
+  return '#$rr$gg$bb';
+}
+
 Color _fromRgbaHex(String eight) {
   final rr = eight.substring(0, 2);
   final gg = eight.substring(2, 4);
diff --git a/lib/core/theme/parser/querya_theme_from_vscode.dart b/lib/core/theme/parser/querya_theme_from_vscode.dart
index 68dfca79..0b5c4c99 100644
--- a/lib/core/theme/parser/querya_theme_from_vscode.dart
+++ b/lib/core/theme/parser/querya_theme_from_vscode.dart
@@ -187,3 +187,21 @@ QueryaEditorTheme _applyEditorField(
       return e.copyWith(foreground: color);
   }
 }
+
+/// Builds [QueryaTheme] from merged VS Code `colors` on top of [fallback].
+QueryaTheme buildQueryaThemeFromVsCodeColors({
+  required Brightness brightness,
+  required Map<String, String> colors,
+  QueryaTheme? fallback,
+}) {
+  final base = fallback ??
+      (brightness == Brightness.light
+          ? QueryaTheme.lightDefault
+          : QueryaTheme.darkDefault);
+  if (colors.isEmpty) return base;
+  final manifest = VsCodeThemeManifest(
+    type: brightness == Brightness.light ? 'light' : 'dark',
+    colors: colors,
+  );
+  return buildQueryaThemeFromVsCodeManifest(manifest, fallback: base);
+}
diff --git a/lib/core/theme/parser/vscode_colors_merge.dart b/lib/core/theme/parser/vscode_colors_merge.dart
new file mode 100644
index 00000000..63269684
--- /dev/null
+++ b/lib/core/theme/parser/vscode_colors_merge.dart
@@ -0,0 +1,14 @@
+// Deep-merge VS Code `colors` maps (later layers override earlier keys).
+
+/// Merges VS Code color layers left-to-right; returns an unmodifiable map.
+///
+/// Typical pipeline: `defaultColors` → `importedColors` → `userOverrides`.
+Map<String, String> mergeVsCodeColorLayers(
+  Iterable<Map<String, String>> layers,
+) {
+  final merged = <String, String>{};
+  for (final layer in layers) {
+    merged.addAll(layer);
+  }
+  return Map.unmodifiable(merged);
+}
diff --git a/lib/core/theme/theme_controller.dart b/lib/core/theme/theme_controller.dart
index fafd0eab..94bea9ad 100644
--- a/lib/core/theme/theme_controller.dart
+++ b/lib/core/theme/theme_controller.dart
@@ -1,10 +1,13 @@
 import 'package:querya_desktop/core/storage/app_settings.dart';
 import 'package:shadcn_flutter/shadcn_flutter.dart';
 
+import 'parser/color_parser.dart';
+import 'parser/querya_theme_from_vscode.dart';
+import 'parser/vscode_colors_merge.dart';
 import 'querya_theme.dart';
 import 'querya_theme_preset.dart';
 
-/// Active theme state: preset + [ThemeMode], persisted via [AppSettings].
+/// Active theme state: preset, optional imported colors, user overrides.
 class ThemeController extends ChangeNotifier {
   ThemeController._();
 
@@ -12,6 +15,8 @@ class ThemeController extends ChangeNotifier {
 
   ThemeMode _themeMode = ThemeMode.dark;
   QueryaThemePreset _preset = QueryaThemePreset.queryaDark;
+  Map<String, String> _importedColors = const {};
+  Map<String, String> _userOverrides = const {};
   bool _loaded = false;
 
   ThemeMode get themeMode => _themeMode;
@@ -20,29 +25,48 @@ class ThemeController extends ChangeNotifier {
 
   bool get isLoaded => _loaded;
 
-  /// Workbench + editor tokens for the current preset/mode.
-  QueryaTheme get activeTheme {
-    if (_themeMode == ThemeMode.system) {
-      final b = WidgetsBinding.instance.platformDispatcher.platformBrightness;
-      return b == Brightness.dark
-          ? QueryaTheme.darkDefault
-          : QueryaTheme.lightDefault;
+  /// User `workbench.colorCustomizations` layer (VS Code keys → hex).
+  Map<String, String> get userColorOverrides =>
+      Map.unmodifiable(_userOverrides);
+
+  /// Imported theme `colors` layer (from file import; empty until wired).
+  Map<String, String> get importedColors => Map.unmodifiable(_importedColors);
+
+  /// Merged VS Code color keys: imported → user overrides.
+  Map<String, String> get effectiveVsCodeColors => mergeVsCodeColorLayers([
+        _importedColors,
+        _userOverrides,
+      ]);
+
+  /// Parsed effective colors for supported VS Code keys only.
+  Map<String, Color> get effectiveWorkbenchColors {
+    final out = <String, Color>{};
+    for (final entry in effectiveVsCodeColors.entries) {
+      try {
+        out[entry.key] = parseVsCodeColor(entry.value);
+      } on FormatException {
+        continue;
+      }
     }
-    return _preset == QueryaThemePreset.queryaLight
-        ? QueryaTheme.lightDefault
-        : QueryaTheme.darkDefault;
+    return Map.unmodifiable(out);
   }
 
+  /// Workbench + editor tokens for the current preset/mode and overrides.
+  QueryaTheme get activeTheme => _themeForBrightness(_effectiveBrightness());
+
   ThemeData get lightShadcnTheme =>
-      QueryaTheme.lightDefault.toShadcnThemeData();
+      _themeForBrightness(Brightness.light).toShadcnThemeData();
 
-  ThemeData get darkShadcnTheme => QueryaTheme.darkDefault.toShadcnThemeData();
+  ThemeData get darkShadcnTheme =>
+      _themeForBrightness(Brightness.dark).toShadcnThemeData();
 
   Future<void> load() async {
     final mode = await AppSettings.instance.getThemeMode();
     final preset = await AppSettings.instance.getThemePreset();
+    final overrides = await AppSettings.instance.getThemeColorOverrides();
     _themeMode = mode;
     _preset = preset;
+    _userOverrides = Map.unmodifiable(overrides);
     _loaded = true;
     notifyListeners();
   }
@@ -67,10 +91,53 @@ class ThemeController extends ChangeNotifier {
     notifyListeners();
   }
 
+  /// Sets or clears a user override for a VS Code `colors` key.
+  Future<void> setWorkbenchColor(String vscodeKey, Color? value) async {
+    final next = Map<String, String>.from(_userOverrides);
+    if (value == null) {
+      next.remove(vscodeKey);
+    } else {
+      next[vscodeKey] = formatVsCodeColor(value);
+    }
+    _userOverrides = Map.unmodifiable(next);
+    await AppSettings.instance.setThemeColorOverrides(next);
+    notifyListeners();
+  }
+
+  /// Removes only the user override layer (keeps preset/imported theme).
+  Future<void> clearColorOverrides() async {
+    _userOverrides = const {};
+    await AppSettings.instance.clearThemeColorOverrides();
+    notifyListeners();
+  }
+
   Future<void> resetToDefaults() async {
     await AppSettings.instance.clearThemeSettings();
     _themeMode = ThemeMode.dark;
     _preset = QueryaThemePreset.queryaDark;
+    _importedColors = const {};
+    _userOverrides = const {};
     notifyListeners();
   }
+
+  Brightness _effectiveBrightness() {
+    if (_themeMode == ThemeMode.system) {
+      final b = WidgetsBinding.instance.platformDispatcher.platformBrightness;
+      return b;
+    }
+    return _themeMode == ThemeMode.light ? Brightness.light : Brightness.dark;
+  }
+
+  QueryaTheme _themeForBrightness(Brightness brightness) {
+    final fallback = brightness == Brightness.light
+        ? QueryaTheme.lightDefault
+        : QueryaTheme.darkDefault;
+    final merged = effectiveVsCodeColors;
+    if (merged.isEmpty) return fallback;
+    return buildQueryaThemeFromVsCodeColors(
+      brightness: brightness,
+      colors: merged,
+      fallback: fallback,
+    );
+  }
 }
diff --git a/test/core/storage/app_settings_test.dart b/test/core/storage/app_settings_test.dart
index 5770cb7a..1b8d60a6 100644
--- a/test/core/storage/app_settings_test.dart
+++ b/test/core/storage/app_settings_test.dart
@@ -200,6 +200,19 @@ void main() {
       await AppSettings.instance.clearThemeSettings();
       expect(await AppSettings.instance.getThemeMode(), ThemeMode.dark);
     });
+
+    test('theme color overrides json roundtrip', () async {
+      await AppSettings.instance.setThemeColorOverrides({
+        'sideBar.background': '#ff0000',
+        'editor.background': '#1e1e1e',
+      });
+      expect(await AppSettings.instance.getThemeColorOverrides(), {
+        'sideBar.background': '#ff0000',
+        'editor.background': '#1e1e1e',
+      });
+      await AppSettings.instance.clearThemeColorOverrides();
+      expect(await AppSettings.instance.getThemeColorOverrides(), isEmpty);
+    });
   });
 
   group('AppSettingsRevision', () {
diff --git a/test/core/theme/parser/color_parser_test.dart b/test/core/theme/parser/color_parser_test.dart
index 014598de..f928edbc 100644
--- a/test/core/theme/parser/color_parser_test.dart
+++ b/test/core/theme/parser/color_parser_test.dart
@@ -1,7 +1,8 @@
 import 'dart:ui';
 
 import 'package:flutter_test/flutter_test.dart';
-import 'package:querya_desktop/core/theme/parser/color_parser.dart';
+import 'package:querya_desktop/core/theme/parser/color_parser.dart'
+    show formatVsCodeColor, parseVsCodeColor;
 
 void main() {
   group('parseVsCodeColor', () {
@@ -26,5 +27,11 @@ void main() {
     test('invalid throws', () {
       expect(() => parseVsCodeColor('nope'), throwsFormatException);
     });
+
+    test('formatVsCodeColor roundtrip', () {
+      const c = Color(0xFF1E1E1E);
+      expect(formatVsCodeColor(c), '#1e1e1e');
+      expect(parseVsCodeColor(formatVsCodeColor(c)), c);
+    });
   });
 }
diff --git a/test/core/theme/parser/querya_theme_merge_pipeline_test.dart b/test/core/theme/parser/querya_theme_merge_pipeline_test.dart
new file mode 100644
index 00000000..df4b7177
--- /dev/null
+++ b/test/core/theme/parser/querya_theme_merge_pipeline_test.dart
@@ -0,0 +1,61 @@
+import 'package:flutter_test/flutter_test.dart';
+import 'package:querya_desktop/core/theme/parser/querya_theme_from_vscode.dart';
+import 'package:querya_desktop/core/theme/parser/vscode_colors_merge.dart';
+import 'package:querya_desktop/core/theme/parser/vscode_theme_manifest.dart';
+import 'package:querya_desktop/core/theme/querya_theme.dart';
+import 'package:shadcn_flutter/shadcn_flutter.dart';
+
+void main() {
+  group('theme merge pipeline', () {
+    test('default → imported → user overrides', () {
+      const defaultLayer = {
+        'editor.background': '#1e1e1e',
+        'sideBar.background': '#252526',
+      };
+      const importedLayer = {
+        'editor.background': '#2d2d30',
+        'sideBar.background': '#333333',
+      };
+      const userLayer = {
+        'sideBar.background': '#ff0000',
+      };
+
+      final merged = mergeVsCodeColorLayers([
+        defaultLayer,
+        importedLayer,
+        userLayer,
+      ]);
+
+      final theme = buildQueryaThemeFromVsCodeColors(
+        brightness: Brightness.dark,
+        colors: merged,
+        fallback: QueryaTheme.darkDefault,
+      );
+
+      expect(theme.workbench.editorBackground, const Color(0xFF2D2D30));
+      expect(theme.workbench.sidebarBackground, const Color(0xFFFF0000));
+    });
+
+    test('manifest import then user override on same key', () {
+      const src = '''
+{
+  "type": "dark",
+  "colors": {
+    "editor.background": "#1e1e1e"
+  }
+}
+''';
+      final imported = VsCodeThemeManifest.fromJsonString(src).colors;
+      final merged = mergeVsCodeColorLayers([
+        imported,
+        {'editor.background': '#abcdef'},
+      ]);
+      final theme = buildQueryaThemeFromVsCodeColors(
+        brightness: Brightness.dark,
+        colors: merged,
+        fallback: QueryaTheme.darkDefault,
+      );
+      expect(theme.workbench.editorBackground, const Color(0xFFABCDEF));
+    });
+  });
+}
diff --git a/test/core/theme/parser/vscode_colors_merge_test.dart b/test/core/theme/parser/vscode_colors_merge_test.dart
new file mode 100644
index 00000000..4bec6971
--- /dev/null
+++ b/test/core/theme/parser/vscode_colors_merge_test.dart
@@ -0,0 +1,31 @@
+import 'package:flutter_test/flutter_test.dart';
+import 'package:querya_desktop/core/theme/parser/vscode_colors_merge.dart';
+
+void main() {
+  group('mergeVsCodeColorLayers', () {
+    test('empty layers yields empty map', () {
+      expect(mergeVsCodeColorLayers([]), isEmpty);
+    });
+
+    test('later layers override earlier keys', () {
+      final merged = mergeVsCodeColorLayers([
+        {'editor.background': '#111111', 'sideBar.background': '#222222'},
+        {'editor.background': '#333333', 'panel.background': '#444444'},
+        {'sideBar.background': '#ff0000'},
+      ]);
+      expect(merged['editor.background'], '#333333');
+      expect(merged['panel.background'], '#444444');
+      expect(merged['sideBar.background'], '#ff0000');
+    });
+
+    test('result is unmodifiable', () {
+      final merged = mergeVsCodeColorLayers([
+        {'a': '#111111'},
+      ]);
+      expect(
+        () => merged['b'] = '#222222',
+        throwsUnsupportedError,
+      );
+    });
+  });
+}
diff --git a/test/core/theme/theme_controller_test.dart b/test/core/theme/theme_controller_test.dart
index 3da820c4..0d4b7e4c 100644
--- a/test/core/theme/theme_controller_test.dart
+++ b/test/core/theme/theme_controller_test.dart
@@ -75,4 +75,37 @@ void main() {
     expect(c.themeMode, ThemeMode.dark);
     expect(c.activeTheme, QueryaTheme.darkDefault);
   });
+
+  test('setWorkbenchColor overrides sidebar and persists', () async {
+    final c = ThemeController.instance;
+    await c.load();
+    await c.setWorkbenchColor(
+      'sideBar.background',
+      const Color(0xFFFF0000),
+    );
+    expect(
+      c.activeTheme.workbench.sidebarBackground,
+      const Color(0xFFFF0000),
+    );
+    expect(
+      (await AppSettings.instance.getThemeColorOverrides())['sideBar.background'],
+      '#ff0000',
+    );
+
+    await c.clearColorOverrides();
+    expect(c.userColorOverrides, isEmpty);
+    expect(
+      c.activeTheme.workbench.sidebarBackground,
+      QueryaTheme.darkDefault.workbench.sidebarBackground,
+    );
+  });
+
+  test('clearColorOverrides does not reset theme mode', () async {
+    final c = ThemeController.instance;
+    await c.setThemeMode(ThemeMode.light);
+    await c.setWorkbenchColor('editor.background', const Color(0xFF111111));
+    await c.clearColorOverrides();
+    expect(c.themeMode, ThemeMode.light);
+    expect(c.activeTheme, QueryaTheme.lightDefault);
+  });
 }