diff --git a/Sources/Panels/BrowserPanel.swift b/Sources/Panels/BrowserPanel.swift
index faf39dea..dfbd8a9c 100644
--- a/Sources/Panels/BrowserPanel.swift
+++ b/Sources/Panels/BrowserPanel.swift
@@ -210,6 +210,17 @@ enum BrowserThemeSettings {
 
         return defaultMode
     }
+
+    static func apply(_ mode: BrowserThemeMode, to webView: WKWebView) {
+        switch mode {
+        case .system:
+            webView.appearance = nil
+        case .light:
+            webView.appearance = NSAppearance(named: .aqua)
+        case .dark:
+            webView.appearance = NSAppearance(named: .darkAqua)
+        }
+    }
 }
 
 enum BrowserImportHintVariant: String, CaseIterable, Identifiable {
@@ -2295,6 +2306,10 @@ final class BrowserPanel: Panel, ObservableObject {
         profileID == BrowserProfileStore.shared.builtInDefaultProfileID
     }
 
+    var currentBrowserThemeMode: BrowserThemeMode {
+        browserThemeMode
+    }
+
     private static let portalHostAreaThreshold: CGFloat = 4
     private static let portalHostReplacementAreaGainRatio: CGFloat = 1.2
 
@@ -2468,8 +2483,9 @@ final class BrowserPanel: Panel, ObservableObject {
         if #available(macOS 13.3, *) {
             webView.isInspectable = true
         }
-        // Match the empty-page background to the terminal theme so newly-created browsers
-        // don't flash white before content loads.
+        // Match only the unpainted/loading background so newly-created browsers don't flash
+        // white before content loads. Do not force page appearance or inject color-scheme CSS;
+        // websites must keep control of their own theme.
         webView.underPageBackgroundColor = GhosttyBackgroundTheme.currentColor()
         // Always present as Safari.
         webView.customUserAgent = BrowserUserAgentSettings.safariUserAgent
@@ -2544,7 +2560,6 @@ final class BrowserPanel: Panel, ObservableObject {
                 self.realignRestoredSessionHistoryToLiveCurrentIfPossible()
                 boundHistoryStore.recordVisit(url: webView.url, title: webView.title)
                 self.refreshFavicon(from: webView)
-                self.applyBrowserThemeModeIfNeeded()
                 // Keep find-in-page open through load completion and refresh matches for the new DOM.
                 self.restoreFindStateAfterNavigation(replaySearch: true)
             }
@@ -4929,6 +4944,9 @@ extension BrowserPanel {
     func setBrowserThemeMode(_ mode: BrowserThemeMode) {
         browserThemeMode = mode
         applyBrowserThemeModeIfNeeded()
+        for controller in popupControllers {
+            controller.setBrowserThemeMode(mode)
+        }
     }
 
     func refreshAppearanceDrivenColors() {
@@ -5431,63 +5449,7 @@ extension BrowserPanel {
 
 private extension BrowserPanel {
     func applyBrowserThemeModeIfNeeded() {
-        switch browserThemeMode {
-        case .system:
-            webView.appearance = nil
-        case .light:
-            webView.appearance = NSAppearance(named: .aqua)
-        case .dark:
-            webView.appearance = NSAppearance(named: .darkAqua)
-        }
-
-        let script = makeBrowserThemeModeScript(mode: browserThemeMode)
-        webView.evaluateJavaScript(script) { _, error in
-            #if DEBUG
-            if let error {
-                dlog("browser.themeMode error=\(error.localizedDescription)")
-            }
-            #endif
-        }
-    }
-
-    func makeBrowserThemeModeScript(mode: BrowserThemeMode) -> String {
-        let colorSchemeLiteral: String
-        switch mode {
-        case .system:
-            colorSchemeLiteral = "null"
-        case .light:
-            colorSchemeLiteral = "'light'"
-        case .dark:
-            colorSchemeLiteral = "'dark'"
-        }
-
-        return """
-        (() => {
-          const metaId = 'cmux-browser-theme-mode-meta';
-          const colorScheme = \(colorSchemeLiteral);
-          const root = document.documentElement || document.body;
-          if (!root) return;
-
-          let meta = document.getElementById(metaId);
-          if (colorScheme) {
-            root.style.setProperty('color-scheme', colorScheme, 'important');
-            root.setAttribute('data-cmux-browser-theme', colorScheme);
-            if (!meta) {
-              meta = document.createElement('meta');
-              meta.id = metaId;
-              meta.name = 'color-scheme';
-              (document.head || root).appendChild(meta);
-            }
-            meta.setAttribute('content', colorScheme);
-          } else {
-            root.style.removeProperty('color-scheme');
-            root.removeAttribute('data-cmux-browser-theme');
-            if (meta) {
-              meta.remove();
-            }
-          }
-        })();
-        """
+        BrowserThemeSettings.apply(browserThemeMode, to: webView)
     }
 
     func scheduleDeveloperToolsRestoreRetry() {
diff --git a/Sources/Panels/BrowserPopupWindowController.swift b/Sources/Panels/BrowserPopupWindowController.swift
index b457ba85..623a9bc9 100644
--- a/Sources/Panels/BrowserPopupWindowController.swift
+++ b/Sources/Panels/BrowserPopupWindowController.swift
@@ -111,6 +111,7 @@ final class BrowserPopupWindowController: NSObject, NSWindowDelegate {
         }
         webView.underPageBackgroundColor = GhosttyBackgroundTheme.currentColor()
         webView.customUserAgent = BrowserUserAgentSettings.safariUserAgent
+        BrowserThemeSettings.apply(openerPanel?.currentBrowserThemeMode ?? BrowserThemeSettings.mode(), to: webView)
         self.webView = webView
 
         // --- Window sizing from WKWindowFeatures ---
@@ -251,6 +252,13 @@ final class BrowserPopupWindowController: NSObject, NSWindowDelegate {
         childPopups.removeAll { $0 === child }
     }
 
+    func setBrowserThemeMode(_ mode: BrowserThemeMode) {
+        BrowserThemeSettings.apply(mode, to: webView)
+        for child in childPopups {
+            child.setBrowserThemeMode(mode)
+        }
+    }
+
     // MARK: - Popup lifecycle
 
     func closePopup() {