diff --git a/components/misc_metrics/brave_search_metrics.cc b/components/misc_metrics/brave_search_metrics.cc
index c7bdc3e4018..0817f3463b6 100644
--- a/components/misc_metrics/brave_search_metrics.cc
+++ b/components/misc_metrics/brave_search_metrics.cc
@@ -16,6 +16,7 @@
 #include "build/build_config.h"
 #include "components/prefs/pref_registry_simple.h"
 #include "components/prefs/pref_service.h"
+#include "components/prefs/scoped_user_pref_update.h"
 #include "components/search_engines/template_url.h"
 #include "components/search_engines/template_url_service.h"
 
@@ -23,8 +24,12 @@ namespace misc_metrics {
 
 namespace {
 
-constexpr int kDailyQueriesBuckets[] = {0, 3, 7};
+// Buckets for DailyQueries. Answers 0 and 1 are reserved for the zero-query
+// cases (no navigation and had navigation respectively), so two dummy leading
+// values push real query counts to indices 2 and above.
+constexpr int kDailyQueriesBuckets[] = {0, 0, 3, 7};
 constexpr char kQueriesCountKey[] = "queries";
+constexpr char kAnyNavigationKey[] = "any_navigation";
 constexpr char kPrimaryQueriesCountKey[] = "primary";
 constexpr char kOmniboxTypedCountKey[] = "omnibox_typed";
 constexpr char kOmniboxSuggestionCountKey[] = "omnibox_suggestion";
@@ -71,6 +76,9 @@ void BraveSearchMetrics::RegisterPrefs(PrefRegistrySimple* registry) {
 
 void BraveSearchMetrics::MaybeRecordBraveQuery(const GURL& previous_url,
                                                const GURL& current_url) {
+  ScopedDictPrefUpdate(local_state_, kMiscMetricsBraveSearchQueryCounts)
+      ->Set(kAnyNavigationKey, true);
+
   if (!IsBraveSearchURL(current_url)) {
     return;
   }
@@ -148,6 +156,7 @@ void BraveSearchMetrics::ReportAllMetrics() {
   const base::DictValue& counts =
       local_state_->GetDict(kMiscMetricsBraveSearchQueryCounts);
   int sum = counts.FindInt(kQueriesCountKey).value_or(0);
+  bool any_navigation = counts.FindBool(kAnyNavigationKey).value_or(false);
 
   auto* histogram_name_ptr =
       base::FindOrNull(kDailyQueriesHistogramMap, engine_type);
@@ -155,7 +164,13 @@ void BraveSearchMetrics::ReportAllMetrics() {
                              ? *histogram_name_ptr
                              : kSearchDailyQueriesOtherDefaultHistogramName;
 
-  p3a_utils::RecordToHistogramBucket(histogram_name, kDailyQueriesBuckets, sum);
+  if (sum == 0) {
+    base::UmaHistogramExactLinear(histogram_name, any_navigation ? 1 : 0,
+                                  std::size(kDailyQueriesBuckets) + 1);
+  } else {
+    p3a_utils::RecordToHistogramBucket(histogram_name, kDailyQueriesBuckets,
+                                       sum);
+  }
 
   int primary_queries = counts.FindInt(kPrimaryQueriesCountKey).value_or(0);
   if (primary_queries > 0) {
diff --git a/components/misc_metrics/brave_search_metrics.h b/components/misc_metrics/brave_search_metrics.h
index 74c72f08c2d..fb7e1e4ce29 100644
--- a/components/misc_metrics/brave_search_metrics.h
+++ b/components/misc_metrics/brave_search_metrics.h
@@ -22,15 +22,15 @@ class TemplateURLService;
 namespace misc_metrics {
 
 inline constexpr char kSearchDailyQueriesBraveDefaultHistogramName[] =
-    "Brave.Search.DailyQueries.BraveDefault";
+    "Brave.Search.DailyQueries.BraveDefault.2";
 inline constexpr char kSearchDailyQueriesGoogleDefaultHistogramName[] =
-    "Brave.Search.DailyQueries.GoogleDefault";
+    "Brave.Search.DailyQueries.GoogleDefault.2";
 inline constexpr char kSearchDailyQueriesDDGDefaultHistogramName[] =
-    "Brave.Search.DailyQueries.DDGDefault";
+    "Brave.Search.DailyQueries.DDGDefault.2";
 inline constexpr char kSearchDailyQueriesYahooDefaultHistogramName[] =
-    "Brave.Search.DailyQueries.YahooDefault";
+    "Brave.Search.DailyQueries.YahooDefault.2";
 inline constexpr char kSearchDailyQueriesOtherDefaultHistogramName[] =
-    "Brave.Search.DailyQueries.OtherDefault";
+    "Brave.Search.DailyQueries.OtherDefault.2";
 inline constexpr char kSearchOmniboxTypedPercentHistogramName[] =
     "Brave.Search.OmniboxTypedPercent";
 inline constexpr char kSearchOmniboxSuggestionPercentHistogramName[] =
diff --git a/components/misc_metrics/brave_search_metrics_unittest.cc b/components/misc_metrics/brave_search_metrics_unittest.cc
index 85d1cef1aa9..440ea3c048b 100644
--- a/components/misc_metrics/brave_search_metrics_unittest.cc
+++ b/components/misc_metrics/brave_search_metrics_unittest.cc
@@ -80,9 +80,11 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesBuckets) {
   // Advance 24 hours then report.
   FastForwardAndReport(base::Days(1));
 
-  // Should report bucket 1 (3 queries -> 1-3 range).
+  // Buckets 0 and 1 are reserved for zero-query cases (no navigation / had
+  // navigation). Real query counts start at index 2.
+  // Should report bucket 2 (3 queries -> 1-3 range).
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesBraveDefaultHistogramName, 1, 1);
+      kSearchDailyQueriesBraveDefaultHistogramName, 2, 1);
   histogram_tester_.ExpectTotalCount(
       kSearchDailyQueriesGoogleDefaultHistogramName, 0);
   histogram_tester_.ExpectTotalCount(
@@ -95,9 +97,9 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesBuckets) {
 
   FastForwardAndReport(base::Days(1));
 
-  // Should report bucket 2 (7 queries -> 4-7 range).
+  // Should report bucket 3 (7 queries -> 4-7 range).
   histogram_tester_.ExpectBucketCount(
-      kSearchDailyQueriesBraveDefaultHistogramName, 2, 1);
+      kSearchDailyQueriesBraveDefaultHistogramName, 3, 1);
 
   // Record 8 queries in the new window.
   for (int i = 0; i < 8; i++) {
@@ -106,9 +108,9 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesBuckets) {
 
   FastForwardAndReport(base::Days(1));
 
-  // Should report bucket 3 (8 queries -> 8+ range).
+  // Should report bucket 4 (8 queries -> 8+ range).
   histogram_tester_.ExpectBucketCount(
-      kSearchDailyQueriesBraveDefaultHistogramName, 3, 1);
+      kSearchDailyQueriesBraveDefaultHistogramName, 4, 1);
 
   histogram_tester_.ExpectTotalCount(
       kSearchDailyQueriesBraveDefaultHistogramName, 3);
@@ -130,9 +132,9 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesEngineSwitch) {
   // Advance past 24 hours then report.
   FastForwardAndReport(base::Days(1));
 
-  // Should report under Google (3 queries -> bucket 1).
+  // Should report under Google (3 queries -> bucket 2, 1-3 range).
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesGoogleDefaultHistogramName, 1, 1);
+      kSearchDailyQueriesGoogleDefaultHistogramName, 2, 1);
   histogram_tester_.ExpectTotalCount(
       kSearchDailyQueriesBraveDefaultHistogramName, 0);
   histogram_tester_.ExpectTotalCount(kSearchDailyQueriesDDGDefaultHistogramName,
@@ -153,13 +155,13 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesEngineSwitch) {
   // Advance past 24 hours then report.
   FastForwardAndReport(base::Days(1));
 
-  // Should report under OtherDefault (5 queries -> bucket 2).
+  // Should report under OtherDefault (5 queries -> bucket 3, 4-7 range).
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesOtherDefaultHistogramName, 2, 1);
+      kSearchDailyQueriesOtherDefaultHistogramName, 3, 1);
   histogram_tester_.ExpectTotalCount(
       kSearchDailyQueriesBraveDefaultHistogramName, 0);
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesGoogleDefaultHistogramName, 1, 1);
+      kSearchDailyQueriesGoogleDefaultHistogramName, 2, 1);
   histogram_tester_.ExpectTotalCount(kSearchDailyQueriesDDGDefaultHistogramName,
                                      0);
   histogram_tester_.ExpectTotalCount(
@@ -176,13 +178,13 @@ TEST_F(BraveSearchMetricsUnitTest, DailyQueriesEngineSwitch) {
   // Advance past 24 hours then report.
   FastForwardAndReport(base::Days(1));
 
-  // Should report under BraveDefault (8 queries -> bucket 3).
+  // Should report under BraveDefault (8 queries -> bucket 4, 8+ range).
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesBraveDefaultHistogramName, 3, 1);
+      kSearchDailyQueriesBraveDefaultHistogramName, 4, 1);
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesOtherDefaultHistogramName, 2, 1);
+      kSearchDailyQueriesOtherDefaultHistogramName, 3, 1);
   histogram_tester_.ExpectUniqueSample(
-      kSearchDailyQueriesGoogleDefaultHistogramName, 1, 1);
+      kSearchDailyQueriesGoogleDefaultHistogramName, 2, 1);
   histogram_tester_.ExpectTotalCount(kSearchDailyQueriesDDGDefaultHistogramName,
                                      0);
   histogram_tester_.ExpectTotalCount(
@@ -195,9 +197,9 @@ TEST_F(BraveSearchMetricsUnitTest, CountsClearedAfterReport) {
   // Advance past 24 hours then report.
   FastForwardAndReport(base::Days(1));
 
-  // Previous window reported 1 query -> bucket 1.
+  // Previous window reported 1 query -> bucket 2 (1-3 range).
   histogram_tester_.ExpectBucketCount(
-      kSearchDailyQueriesBraveDefaultHistogramName, 1, 1);
+      kSearchDailyQueriesBraveDefaultHistogramName, 2, 1);
 
   // Record 1 query in the new window.
   brave_search_metrics_->MaybeRecordBraveQuery(empty_url_, brave_search_url_);
@@ -207,7 +209,7 @@ TEST_F(BraveSearchMetricsUnitTest, CountsClearedAfterReport) {
 
   // Should report 1 query again for the new window.
   histogram_tester_.ExpectBucketCount(
-      kSearchDailyQueriesBraveDefaultHistogramName, 1, 2);
+      kSearchDailyQueriesBraveDefaultHistogramName, 2, 2);
 }
 
 TEST_F(BraveSearchMetricsUnitTest, ClearQueryCounts) {
@@ -224,11 +226,36 @@ TEST_F(BraveSearchMetricsUnitTest, ClearQueryCounts) {
   // Advance past 24 hours and report.
   FastForwardAndReport(base::Days(1));
 
-  // Should report bucket 0 (0 queries) since counts were cleared.
+  // Counts cleared means sum=0 and any_navigation=false -> bucket 0.
   histogram_tester_.ExpectUniqueSample(
       kSearchDailyQueriesBraveDefaultHistogramName, 0, 1);
 }
 
+TEST_F(BraveSearchMetricsUnitTest, DailyQueriesNoNavigationReportsZero) {
+  // No queries and no navigation in this window -> bucket 0.
+  FastForwardAndReport(base::Days(1));
+  histogram_tester_.ExpectUniqueSample(
+      kSearchDailyQueriesBraveDefaultHistogramName, 0, 1);
+
+  // After reset, another empty window also reports bucket 0.
+  FastForwardAndReport(base::Days(1));
+  histogram_tester_.ExpectBucketCount(
+      kSearchDailyQueriesBraveDefaultHistogramName, 0, 2);
+}
+
+TEST_F(BraveSearchMetricsUnitTest,
+       DailyQueriesNavigationButNoSearchReportsOne) {
+  // Navigate to a non-search URL: sets any_navigation=true but sum stays 0.
+  const GURL non_search_url{"https://example.com"};
+  brave_search_metrics_->MaybeRecordBraveQuery(empty_url_, non_search_url);
+
+  FastForwardAndReport(base::Days(1));
+
+  // any_navigation=true, sum=0 -> bucket 1.
+  histogram_tester_.ExpectUniqueSample(
+      kSearchDailyQueriesBraveDefaultHistogramName, 1, 1);
+}
+
 TEST_F(BraveSearchMetricsUnitTest, NoReportBeforeFrameExpires) {
   // Record queries within the 24-hour window.
   for (int i = 0; i < 5; i++) {
diff --git a/components/p3a/metric_names.h b/components/p3a/metric_names.h
index 5f6030bee9d..87d36758345 100644
--- a/components/p3a/metric_names.h
+++ b/components/p3a/metric_names.h
@@ -274,27 +274,27 @@ inline constexpr auto kCollectedExpressHistograms =
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kAnswerIndex, MetricAttribute::kVersion, MetricAttribute::kChannel, MetricAttribute::kPlatform, MetricAttribute::kCountryCode},
     }},
-    {"Brave.Search.DailyQueries.BraveDefault", MetricConfig{
+    {"Brave.Search.DailyQueries.BraveDefault.2", MetricConfig{
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kIsBrowserDefault, MetricAttribute::kAnswerIndex, MetricAttribute::kCustomAttribute, MetricAttribute::kCountryCode, MetricAttribute::kPlatform, MetricAttribute::kYoi},
       .custom_attributes = {"media_session_usage"},
     }},
-    {"Brave.Search.DailyQueries.DDGDefault", MetricConfig{
+    {"Brave.Search.DailyQueries.DDGDefault.2", MetricConfig{
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kIsBrowserDefault, MetricAttribute::kAnswerIndex, MetricAttribute::kCustomAttribute, MetricAttribute::kCountryCode, MetricAttribute::kPlatform, MetricAttribute::kYoi},
       .custom_attributes = {"media_session_usage"},
     }},
-    {"Brave.Search.DailyQueries.GoogleDefault", MetricConfig{
+    {"Brave.Search.DailyQueries.GoogleDefault.2", MetricConfig{
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kIsBrowserDefault, MetricAttribute::kAnswerIndex, MetricAttribute::kCustomAttribute, MetricAttribute::kCountryCode, MetricAttribute::kPlatform, MetricAttribute::kYoi},
       .custom_attributes = {"media_session_usage"},
     }},
-    {"Brave.Search.DailyQueries.OtherDefault", MetricConfig{
+    {"Brave.Search.DailyQueries.OtherDefault.2", MetricConfig{
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kIsBrowserDefault, MetricAttribute::kAnswerIndex, MetricAttribute::kCustomAttribute, MetricAttribute::kCountryCode, MetricAttribute::kPlatform, MetricAttribute::kYoi},
       .custom_attributes = {"media_session_usage"},
     }},
-    {"Brave.Search.DailyQueries.YahooDefault", MetricConfig{
+    {"Brave.Search.DailyQueries.YahooDefault.2", MetricConfig{
       .ephemeral = true,
       .attributes = MetricAttributes{MetricAttribute::kIsBrowserDefault, MetricAttribute::kAnswerIndex, MetricAttribute::kCustomAttribute, MetricAttribute::kCountryCode, MetricAttribute::kPlatform, MetricAttribute::kYoi},
       .custom_attributes = {"media_session_usage"},