diff --git a/browser/new_tab/background_color_tab_helper_browsertest.cc b/browser/new_tab/background_color_tab_helper_browsertest.cc
index ba52da96ad26..3bbbd2292dc0 100644
--- a/browser/new_tab/background_color_tab_helper_browsertest.cc
+++ b/browser/new_tab/background_color_tab_helper_browsertest.cc
@@ -6,6 +6,8 @@
 #include "base/test/scoped_feature_list.h"
 #include "brave/browser/themes/brave_dark_mode_utils.h"
 #include "brave/browser/ui/brave_ui_features.h"
+#include "chrome/browser/ui/color/chrome_color_id.h"
+#include "chrome/browser/ui/views/frame/browser_view.h"
 #include "chrome/common/webui_url_constants.h"
 #include "chrome/test/base/chrome_test_utils.h"
 #include "chrome/test/base/in_process_browser_test.h"
@@ -13,25 +15,21 @@
 #include "content/public/browser/render_widget_host_view.h"
 #include "content/public/test/browser_test.h"
 #include "content/public/test/browser_test_utils.h"
+#include "ui/aura/window.h"
+#include "ui/aura/window_tree_host.h"
+#include "ui/color/color_provider.h"
+#include "ui/compositor/compositor.h"
+#include "ui/gfx/native_widget_types.h"
 
 class BackgroundColorTabHelperBrowserTest
     : public InProcessBrowserTest,
       public testing::WithParamInterface<bool> {
  public:
   BackgroundColorTabHelperBrowserTest() {
-    dark_mode::SetUseSystemDarkModeEnabledForTest(false);
     scoped_feature_list_.InitAndEnableFeature(
         features::kBraveWorkaroundNewWindowFlash);
   }
 
-  void SetUpOnMainThread() override {
-    InProcessBrowserTest::SetUpOnMainThread();
-    dark_mode::SetBraveDarkModeType(
-        IsDarkMode()
-            ? dark_mode::BraveDarkModeType::BRAVE_DARK_MODE_TYPE_DARK
-            : dark_mode::BraveDarkModeType::BRAVE_DARK_MODE_TYPE_LIGHT);
-  }
-
   content::WebContents* web_contents() {
     return chrome_test_utils::GetActiveWebContents(this);
   }
@@ -42,6 +40,13 @@ class BackgroundColorTabHelperBrowserTest
   base::test::ScopedFeatureList scoped_feature_list_;
 };
 
+IN_PROC_BROWSER_TEST_P(BackgroundColorTabHelperBrowserTest,
+                       PRE_BackgroundColorIsSet) {
+  dark_mode::SetBraveDarkModeType(
+      IsDarkMode() ? dark_mode::BraveDarkModeType::BRAVE_DARK_MODE_TYPE_DARK
+                   : dark_mode::BraveDarkModeType::BRAVE_DARK_MODE_TYPE_LIGHT);
+}
+
 IN_PROC_BROWSER_TEST_P(BackgroundColorTabHelperBrowserTest,
                        BackgroundColorIsSet) {
   ui_test_utils::NavigateToURLWithDisposition(
@@ -49,14 +54,29 @@ IN_PROC_BROWSER_TEST_P(BackgroundColorTabHelperBrowserTest,
       WindowOpenDisposition::NEW_FOREGROUND_TAB,
       ui_test_utils::BROWSER_TEST_WAIT_FOR_LOAD_STOP);
 
-  const auto view_background_color =
-      web_contents()->GetPrimaryMainFrame()->GetView()->GetBackgroundColor();
+  // Expected colors:
+  const auto expected_tab_background_color =
+      web_contents()->GetColorProvider().GetColor(kColorNewTabPageBackground);
 
-  if (IsDarkMode()) {
-    EXPECT_NE(view_background_color, SK_ColorWHITE);
-  } else {
-    EXPECT_EQ(view_background_color, SK_ColorWHITE);
-  }
+  const auto expected_view_host_background_color =
+      web_contents()->GetColorProvider().GetColor(kColorToolbar);
+
+  // Actual colors:
+  const auto tab_background_color =
+      web_contents()->GetTopLevelRenderWidgetHostView()->GetBackgroundColor();
+
+  const auto view_host_background_color =
+      BrowserView::GetBrowserViewForBrowser(browser())
+          ->GetWidget()
+          ->GetNativeView()
+          ->GetHost()
+          ->compositor()
+          ->host_for_testing()
+          ->background_color()
+          .toSkColor();
+
+  EXPECT_EQ(tab_background_color, expected_tab_background_color);
+  EXPECT_EQ(view_host_background_color, expected_view_host_background_color);
 }
 
 INSTANTIATE_TEST_SUITE_P(,
diff --git a/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.cc b/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.cc
index 78c61435ea42..085038412de0 100644
--- a/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.cc
+++ b/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.cc
@@ -39,8 +39,7 @@ bool BrowserDesktopWindowTreeHostWin::PreHandleMSG(UINT message,
       break;
     }
     case WM_NCPAINT: {
-      // If the window is cloacked, fill it with the ntp background color and
-      // uncloak.
+      // If the window is cloacked, fill it with the toolbar color and uncloak.
       if (is_cloacked_ && base::FeatureList::IsEnabled(
                               features::kBraveWorkaroundNewWindowFlash)) {
         HWND hwnd = GetHWND();
@@ -54,8 +53,7 @@ bool BrowserDesktopWindowTreeHostWin::PreHandleMSG(UINT message,
             window_rect.bottom - window_rect.top,
         };
 
-        SkColor bg_color = GetWidget()->GetColorProvider()->GetColor(
-            kColorNewTabPageBackground);
+        SkColor bg_color = GetToolbarColor();
         HBRUSH brush = ::CreateSolidBrush(skia::SkColorToCOLORREF(bg_color));
         ::FillRect(dc, &fill_rect, brush);
         ::DeleteObject(brush);
@@ -71,6 +69,21 @@ bool BrowserDesktopWindowTreeHostWin::PreHandleMSG(UINT message,
       message, w_param, l_param, result);
 }
 
+SkColor BrowserDesktopWindowTreeHostWin::GetBackgroundColor(
+    SkColor requested_color) const {
+  if (requested_color == SK_ColorTRANSPARENT ||
+      !base::FeatureList::IsEnabled(features::kBraveWorkaroundNewWindowFlash)) {
+    return requested_color;
+  }
+
+  return GetToolbarColor();
+}
+
+SkColor BrowserDesktopWindowTreeHostWin::GetToolbarColor() const {
+  CHECK(base::FeatureList::IsEnabled(features::kBraveWorkaroundNewWindowFlash));
+  return GetWidget()->GetColorProvider()->GetColor(kColorToolbar);
+}
+
 // static
 BrowserDesktopWindowTreeHost*
 BrowserDesktopWindowTreeHost::CreateBrowserDesktopWindowTreeHost(
diff --git a/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.h b/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.h
index eeca32f7839f..ee7a41c60343 100644
--- a/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.h
+++ b/chromium_src/chrome/browser/ui/views/frame/browser_desktop_window_tree_host_win.h
@@ -34,6 +34,12 @@ class BrowserDesktopWindowTreeHostWin
                     LPARAM l_param,
                     LRESULT* result) override;
 
+  // Returns the optionally modified background color to correctly match the
+  // toolbar color in dark/private browsing modes.
+  SkColor GetBackgroundColor(SkColor requested_color) const override;
+
+  SkColor GetToolbarColor() const;
+
   bool is_cloacked_ = false;
 };
 
diff --git a/chromium_src/ui/views/widget/desktop_aura/desktop_native_widget_aura.cc b/chromium_src/ui/views/widget/desktop_aura/desktop_native_widget_aura.cc
new file mode 100644
index 000000000000..2979ea2306d6
--- /dev/null
+++ b/chromium_src/ui/views/widget/desktop_aura/desktop_native_widget_aura.cc
@@ -0,0 +1,15 @@
+/* Copyright (c) 2024 The Brave Authors. All rights reserved.
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this file,
+ * You can obtain one at https://mozilla.org/MPL/2.0/. */
+
+#include "ui/views/widget/desktop_aura/desktop_native_widget_aura.h"
+
+#include "ui/compositor/compositor.h"
+
+#define SetBackgroundColor(color) \
+  SetBackgroundColor(desktop_window_tree_host_->GetBackgroundColor(color))
+
+#include "src/ui/views/widget/desktop_aura/desktop_native_widget_aura.cc"
+
+#undef SetBackgroundColor
diff --git a/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.cc b/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.cc
new file mode 100644
index 000000000000..53f39342a6ba
--- /dev/null
+++ b/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.cc
@@ -0,0 +1,17 @@
+/* Copyright (c) 2024 The Brave Authors. All rights reserved.
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this file,
+ * You can obtain one at https://mozilla.org/MPL/2.0/. */
+
+#include "ui/views/widget/desktop_aura/desktop_window_tree_host.h"
+
+#include "src/ui/views/widget/desktop_aura/desktop_window_tree_host.cc"
+
+namespace views {
+
+SkColor DesktopWindowTreeHost::GetBackgroundColor(
+    SkColor requested_color) const {
+  return requested_color;
+}
+
+}  // namespace views
diff --git a/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.h b/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.h
new file mode 100644
index 000000000000..c4c63352b21e
--- /dev/null
+++ b/chromium_src/ui/views/widget/desktop_aura/desktop_window_tree_host.h
@@ -0,0 +1,17 @@
+/* Copyright (c) 2024 The Brave Authors. All rights reserved.
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this file,
+ * You can obtain one at https://mozilla.org/MPL/2.0/. */
+
+#ifndef BRAVE_CHROMIUM_SRC_UI_VIEWS_WIDGET_DESKTOP_AURA_DESKTOP_WINDOW_TREE_HOST_H_
+#define BRAVE_CHROMIUM_SRC_UI_VIEWS_WIDGET_DESKTOP_AURA_DESKTOP_WINDOW_TREE_HOST_H_
+
+#define GetSingletonDesktopNativeCursorManager() \
+  GetSingletonDesktopNativeCursorManager();      \
+  virtual SkColor GetBackgroundColor(SkColor requested_color) const
+
+#include "src/ui/views/widget/desktop_aura/desktop_window_tree_host.h"  // IWYU pragma: export
+
+#undef GetSingletonDesktopNativeCursorManager
+
+#endif  // BRAVE_CHROMIUM_SRC_UI_VIEWS_WIDGET_DESKTOP_AURA_DESKTOP_WINDOW_TREE_HOST_H_