diff --git a/components/web_discovery/browser/BUILD.gn b/components/web_discovery/browser/BUILD.gn
index 2edd60e651bf..24bca33cba88 100644
--- a/components/web_discovery/browser/BUILD.gn
+++ b/components/web_discovery/browser/BUILD.gn
@@ -15,6 +15,7 @@ static_library("browser") {
   deps = [
     ":internal",
     "//base",
+    "//brave/components/web_discovery/common:mojom",
     "//components/keyed_service/core",
     "//components/prefs",
     "//services/network/public/cpp",
@@ -53,9 +54,9 @@ source_set("internal") {
   ]
 
   visibility = [
+    "//brave/browser/web_discovery:browser_tests",
     "//brave/components/web_discovery/browser",
     "//brave/components/web_discovery/browser:unit_tests",
-    "//brave/browser/web_discovery:browser_tests",
   ]
 
   deps = [
diff --git a/components/web_discovery/browser/content_scraper.h b/components/web_discovery/browser/content_scraper.h
index a4454d6e1d04..779f2587ec6f 100644
--- a/components/web_discovery/browser/content_scraper.h
+++ b/components/web_discovery/browser/content_scraper.h
@@ -13,7 +13,7 @@
 #include "base/containers/flat_map.h"
 #include "base/functional/callback.h"
 #include "base/values.h"
-#include "brave/components/web_discovery/browser/document_extractor/src/lib.rs.h"
+#include "brave/components/web_discovery/browser/document_extractor/lib.rs.h"
 #include "brave/components/web_discovery/browser/patterns.h"
 #include "brave/components/web_discovery/browser/server_config_loader.h"
 #include "brave/components/web_discovery/common/web_discovery.mojom.h"
diff --git a/components/web_discovery/browser/hash_detection.cc b/components/web_discovery/browser/hash_detection.cc
index e28762b9b869..4442860016b0 100644
--- a/components/web_discovery/browser/hash_detection.cc
+++ b/components/web_discovery/browser/hash_detection.cc
@@ -35,6 +35,10 @@ constexpr double kClassifierThreshold = 0.015;
 bool IsHashLikely(std::string value, double threshold_multiplier) {
   TransformToAlphanumeric(value);
 
+  if (value.empty()) {
+    return false;
+  }
+
   double log_prob_sum = 0.0;
   size_t add_count = 0;
   for (size_t i = 0; i < value.length() - 1; i++) {
diff --git a/components/web_discovery/browser/hash_detection_unittest.cc b/components/web_discovery/browser/hash_detection_unittest.cc
index 44e2104e91bb..c629a064cc9d 100644
--- a/components/web_discovery/browser/hash_detection_unittest.cc
+++ b/components/web_discovery/browser/hash_detection_unittest.cc
@@ -1,4 +1,3 @@
-
 /* 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,
diff --git a/components/web_discovery/renderer/blink_document_extractor.cc b/components/web_discovery/renderer/blink_document_extractor.cc
index b7fb01114b50..7a7ab2865778 100644
--- a/components/web_discovery/renderer/blink_document_extractor.cc
+++ b/components/web_discovery/renderer/blink_document_extractor.cc
@@ -60,6 +60,9 @@ BlinkDocumentExtractor::BlinkDocumentExtractor(
     content::RenderFrame* render_frame,
     service_manager::BinderRegistry* registry)
     : content::RenderFrameObserver(render_frame), render_frame_(render_frame) {
+  if (!render_frame->IsMainFrame()) {
+    return;
+  }
   registry->AddInterface<mojom::DocumentExtractor>(base::BindRepeating(
       &BlinkDocumentExtractor::BindReceiver, base::Unretained(this)));
 }
diff --git a/renderer/brave_content_renderer_client.cc b/renderer/brave_content_renderer_client.cc
index e45ded956b47..fc164cd98db9 100644
--- a/renderer/brave_content_renderer_client.cc
+++ b/renderer/brave_content_renderer_client.cc
@@ -220,7 +220,8 @@ void BraveContentRendererClient::RenderFrameCreated(
 
 #if BUILDFLAG(ENABLE_WEB_DISCOVERY_NATIVE)
   if (base::FeatureList::IsEnabled(
-          web_discovery::features::kBraveWebDiscoveryNative)) {
+          web_discovery::features::kBraveWebDiscoveryNative) &&
+      !IsIncognitoProcess()) {
     new web_discovery::BlinkDocumentExtractor(render_frame, registry);
   }
 #endif