diff --git a/browser/net/brave_site_hacks_network_delegate_helper.cc b/browser/net/brave_site_hacks_network_delegate_helper.cc
index 6aa29531c45..d0281b4528d 100644
--- a/browser/net/brave_site_hacks_network_delegate_helper.cc
+++ b/browser/net/brave_site_hacks_network_delegate_helper.cc
@@ -94,6 +94,11 @@ DECLARE_LAZY_MATCHER(tracker_appended_matcher,
 void ApplyPotentialQueryStringFilter(std::shared_ptr<BraveRequestInfo> ctx) {
   SCOPED_UMA_HISTOGRAM_TIMER("Brave.SiteHacks.QueryFilter");
 
+  if (!ctx->allow_brave_shields) {
+    // Don't apply the filter if the destination URL has shields down.
+    return;
+  }
+
   if (ctx->redirect_source.is_valid()) {
     if (ctx->internal_redirect) {
       // Ignore internal redirects since we trigger them.
diff --git a/browser/net/brave_site_hacks_network_delegate_helper_browsertest.cc b/browser/net/brave_site_hacks_network_delegate_helper_browsertest.cc
index ca2cae9ea6a..21ead2938ab 100644
--- a/browser/net/brave_site_hacks_network_delegate_helper_browsertest.cc
+++ b/browser/net/brave_site_hacks_network_delegate_helper_browsertest.cc
@@ -7,9 +7,13 @@
 #include "base/path_service.h"
 #include "base/strings/stringprintf.h"
 #include "brave/common/brave_paths.h"
+#include "brave/components/brave_shields/browser/brave_shields_util.h"
+#include "chrome/browser/content_settings/host_content_settings_map_factory.h"
+#include "chrome/browser/profiles/profile.h"
 #include "chrome/browser/ui/browser.h"
 #include "chrome/test/base/in_process_browser_test.h"
 #include "chrome/test/base/ui_test_utils.h"
+#include "components/content_settings/core/browser/host_content_settings_map.h"
 #include "components/network_session_configurator/common/network_switches.h"
 #include "content/public/test/browser_test.h"
 #include "content/public/test/browser_test_utils.h"
@@ -46,6 +50,10 @@ class BraveSiteHacksNetworkDelegateBrowserTest : public InProcessBrowserTest {
         https_server_.GetURL("sub.a.com", "/navigate-to-site.html");
   }
 
+  HostContentSettingsMap* content_settings() {
+    return HostContentSettingsMapFactory::GetForProfile(browser()->profile());
+  }
+
   void SetUpCommandLine(base::CommandLine* command_line) override {
     InProcessBrowserTest::SetUpCommandLine(command_line);
     // This is needed to load pages from "domain.com" without an interstitial.
@@ -141,6 +149,21 @@ IN_PROC_BROWSER_TEST_F(BraveSiteHacksNetworkDelegateBrowserTest,
   }
 }
 
+IN_PROC_BROWSER_TEST_F(BraveSiteHacksNetworkDelegateBrowserTest,
+                       QueryStringFilterShieldsDown) {
+  const std::string inputs[] = {
+      "", "foo=bar", "fbclid=1", "fbclid=2&key=value", "key=value&fbclid=3",
+  };
+
+  constexpr size_t input_count = base::size(inputs);
+
+  for (size_t i = 0; i < input_count; i++) {
+    const GURL dest_url = landing_url(inputs[i], simple_landing_url());
+    brave_shields::SetBraveShieldsEnabled(content_settings(), false, dest_url);
+    NavigateToURLAndWaitForRedirects(url(dest_url, cross_site_url()), dest_url);
+  }
+}
+
 IN_PROC_BROWSER_TEST_F(BraveSiteHacksNetworkDelegateBrowserTest,
                        QueryStringFilterSameSite) {
   const std::string inputs[] = {