diff --git a/app/notification_push.go b/app/notification_push.go
index 757764c613..a50b16ceab 100644
--- a/app/notification_push.go
+++ b/app/notification_push.go
@@ -219,30 +219,42 @@ func (a *App) getPushNotificationMessage(contentsConfig, postMessage string, exp
 	return senderName + userLocale("api.post.send_notifications_and_forget.push_general_message")
 }
 
+func (a *App) getUserBadgeCount(userID string, isCRTEnabled bool) (int, *model.AppError) {
+	unreadCount, err := a.Srv().Store.User().GetUnreadCount(userID, isCRTEnabled)
+	if err != nil {
+		return 0, model.NewAppError("getUserBadgeCount", "app.user.get_unread_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
+	}
+	badgeCount := int(unreadCount)
+
+	if isCRTEnabled {
+		threadUnreadMentions, err := a.Srv().Store.Thread().GetTotalUnreadMentions(userID, "", model.GetUserThreadsOpts{})
+		if err != nil {
+			return 0, model.NewAppError("getUserBadgeCount", "app.user.get_thread_count_for_user.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
+		}
+		badgeCount += int(threadUnreadMentions)
+	}
+
+	return badgeCount, nil
+}
+
 func (a *App) clearPushNotificationSync(c request.CTX, currentSessionId, userID, channelID, rootID string) *model.AppError {
+	isCRTEnabled := a.IsCRTEnabledForUser(c, userID)
+
+	badgeCount, err := a.getUserBadgeCount(userID, isCRTEnabled)
+	if err != nil {
+		return model.NewAppError("clearPushNotificationSync", "app.user.get_badge_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
+	}
+
 	msg := &model.PushNotification{
 		Type:             model.PushTypeClear,
 		Version:          model.PushMessageV2,
 		ChannelId:        channelID,
 		RootId:           rootID,
 		ContentAvailable: 1,
-		Badge:            0,
-		IsCRTEnabled:     a.IsCRTEnabledForUser(c, userID),
+		Badge:            badgeCount,
+		IsCRTEnabled:     isCRTEnabled,
 	}
 
-	unreadCount, err := a.Srv().Store.User().GetUnreadCount(userID)
-	if err != nil {
-		return model.NewAppError("clearPushNotificationSync", "app.user.get_unread_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
-	}
-	msg.Badge = int(unreadCount)
-
-	if msg.IsCRTEnabled {
-		totalUnreadMentions, err := a.Srv().Store.Thread().GetTotalUnreadMentions(userID, "", model.GetUserThreadsOpts{})
-		if err != nil {
-			return model.NewAppError("clearPushNotificationSync", "app.user.get_thread_count_for_user.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
-		}
-		msg.Badge += int(totalUnreadMentions)
-	}
 	return a.sendPushNotificationToAllSessions(msg, userID, currentSessionId)
 }
 
@@ -260,21 +272,19 @@ func (a *App) clearPushNotification(currentSessionId, userID, channelID, rootID
 	}
 }
 
-func (a *App) updateMobileAppBadgeSync(userID string) *model.AppError {
+func (a *App) updateMobileAppBadgeSync(c request.CTX, userID string) *model.AppError {
+	badgeCount, err := a.getUserBadgeCount(userID, a.IsCRTEnabledForUser(c, userID))
+	if err != nil {
+		return model.NewAppError("updateMobileAppBadgeSync", "app.user.get_badge_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
+	}
+
 	msg := &model.PushNotification{
 		Type:             model.PushTypeUpdateBadge,
 		Version:          model.PushMessageV2,
 		Sound:            "none",
 		ContentAvailable: 1,
+		Badge:            badgeCount,
 	}
-
-	unreadCount, err := a.Srv().Store.User().GetUnreadCount(userID)
-	if err != nil {
-		return model.NewAppError("updateMobileAppBadgeSync", "app.user.get_unread_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
-	}
-
-	msg.Badge = int(unreadCount)
-
 	return a.sendPushNotificationToAllSessions(msg, userID, "")
 }
 
@@ -345,7 +355,7 @@ func (hub *PushNotificationsHub) start(c request.CTX) {
 						notification.replyToThreadType,
 					)
 				case notificationTypeUpdateBadge:
-					err = hub.app.updateMobileAppBadgeSync(notification.userID)
+					err = hub.app.updateMobileAppBadgeSync(c, notification.userID)
 				default:
 					mlog.Debug("Invalid notification type", mlog.String("notification_type", string(notification.notificationType)))
 				}
@@ -566,11 +576,12 @@ func (a *App) BuildPushNotificationMessage(c request.CTX, contentsConfig string,
 		msg = a.buildFullPushNotificationMessage(c, contentsConfig, post, user, channel, channelName, senderName, explicitMention, channelWideMention, replyToThreadType)
 	}
 
-	unreadCount, err := a.Srv().Store.User().GetUnreadCount(user.Id)
+	badgeCount, err := a.getUserBadgeCount(user.Id, a.IsCRTEnabledForUser(c, user.Id))
 	if err != nil {
-		return nil, model.NewAppError("BuildPushNotificationMessage", "app.user.get_unread_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
+		return nil, model.NewAppError("BuildPushNotificationMessage", "app.user.get_badge_count.app_error", nil, "", http.StatusInternalServerError).Wrap(err)
 	}
-	msg.Badge = int(unreadCount)
+
+	msg.Badge = badgeCount
 
 	return msg, nil
 }
diff --git a/app/notification_push_test.go b/app/notification_push_test.go
index 0f3e8a157f..dfb226573e 100644
--- a/app/notification_push_test.go
+++ b/app/notification_push_test.go
@@ -1136,7 +1136,7 @@ func TestClearPushNotificationSync(t *testing.T) {
 	mockStore := th.App.Srv().Store.(*mocks.Store)
 	mockUserStore := mocks.UserStore{}
 	mockUserStore.On("Count", mock.Anything).Return(int64(10), nil)
-	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string")).Return(int64(1), nil)
+	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string"), mock.AnythingOfType("bool")).Return(int64(1), nil)
 	mockPostStore := mocks.PostStore{}
 	mockPostStore.On("GetMaxPostSize").Return(65535, nil)
 	mockSystemStore := mocks.SystemStore{}
@@ -1212,7 +1212,7 @@ func TestUpdateMobileAppBadgeSync(t *testing.T) {
 	mockStore := th.App.Srv().Store.(*mocks.Store)
 	mockUserStore := mocks.UserStore{}
 	mockUserStore.On("Count", mock.Anything).Return(int64(10), nil)
-	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string")).Return(int64(1), nil)
+	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string"), mock.AnythingOfType("bool")).Return(int64(1), nil)
 	mockPostStore := mocks.PostStore{}
 	mockPostStore.On("GetMaxPostSize").Return(65535, nil)
 	mockSystemStore := mocks.SystemStore{}
@@ -1231,9 +1231,10 @@ func TestUpdateMobileAppBadgeSync(t *testing.T) {
 
 	th.App.UpdateConfig(func(cfg *model.Config) {
 		*cfg.EmailSettings.PushNotificationServer = pushServer.URL
+		*cfg.ServiceSettings.CollapsedThreads = model.CollapsedThreadsDisabled
 	})
 
-	err := th.App.updateMobileAppBadgeSync("user1")
+	err := th.App.updateMobileAppBadgeSync(th.Context, "user1")
 	require.Nil(t, err)
 	// Server side verification.
 	// We verify that 2 requests have been sent, and also check the message contents.
@@ -1529,7 +1530,7 @@ func BenchmarkPushNotificationThroughput(b *testing.B) {
 	mockStore := th.App.Srv().Store.(*mocks.Store)
 	mockUserStore := mocks.UserStore{}
 	mockUserStore.On("Count", mock.Anything).Return(int64(10), nil)
-	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string")).Return(int64(1), nil)
+	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string"), mock.AnythingOfType("bool")).Return(int64(1), nil)
 	mockPostStore := mocks.PostStore{}
 	mockPostStore.On("GetMaxPostSize").Return(65535, nil)
 	mockSystemStore := mocks.SystemStore{}
diff --git a/app/web_hub_test.go b/app/web_hub_test.go
index f4f347cb7f..e53a2b51d0 100644
--- a/app/web_hub_test.go
+++ b/app/web_hub_test.go
@@ -135,7 +135,7 @@ func TestHubSessionRevokeRace(t *testing.T) {
 
 	mockUserStore := mocks.UserStore{}
 	mockUserStore.On("Count", mock.Anything).Return(int64(10), nil)
-	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string")).Return(int64(1), nil)
+	mockUserStore.On("GetUnreadCount", mock.AnythingOfType("string"), mock.AnythingOfType("bool")).Return(int64(1), nil)
 	mockPostStore := mocks.PostStore{}
 	mockPostStore.On("GetMaxPostSize").Return(65535, nil)
 	mockSystemStore := mocks.SystemStore{}
diff --git a/i18n/en.json b/i18n/en.json
index abf4c2280a..93666a3143 100644
--- a/i18n/en.json
+++ b/i18n/en.json
@@ -6591,6 +6591,10 @@
     "id": "app.user.get.app_error",
     "translation": "We encountered an error finding the account."
   },
+  {
+    "id": "app.user.get_badge_count.app_error",
+    "translation": "We could not get the badge count for the user."
+  },
   {
     "id": "app.user.get_by_auth.missing_account.app_error",
     "translation": "Unable to find an existing account matching your authentication type for this team. This team may require an invite from the team owner to join."
diff --git a/store/opentracinglayer/opentracinglayer.go b/store/opentracinglayer/opentracinglayer.go
index 51a2dd1055..45b6277728 100644
--- a/store/opentracinglayer/opentracinglayer.go
+++ b/store/opentracinglayer/opentracinglayer.go
@@ -11089,7 +11089,7 @@ func (s *OpenTracingLayerUserStore) GetTeamGroupUsers(teamID string) ([]*model.U
 	return result, err
 }
 
-func (s *OpenTracingLayerUserStore) GetUnreadCount(userID string) (int64, error) {
+func (s *OpenTracingLayerUserStore) GetUnreadCount(userID string, isCRTEnabled bool) (int64, error) {
 	origCtx := s.Root.Store.Context()
 	span, newCtx := tracing.StartSpanWithParentByContext(s.Root.Store.Context(), "UserStore.GetUnreadCount")
 	s.Root.Store.SetContext(newCtx)
@@ -11098,7 +11098,7 @@ func (s *OpenTracingLayerUserStore) GetUnreadCount(userID string) (int64, error)
 	}()
 
 	defer span.Finish()
-	result, err := s.UserStore.GetUnreadCount(userID)
+	result, err := s.UserStore.GetUnreadCount(userID, isCRTEnabled)
 	if err != nil {
 		span.LogFields(spanlog.Error(err))
 		ext.Error.Set(span, true)
diff --git a/store/retrylayer/retrylayer.go b/store/retrylayer/retrylayer.go
index 2506d610f9..6e544138a2 100644
--- a/store/retrylayer/retrylayer.go
+++ b/store/retrylayer/retrylayer.go
@@ -12660,11 +12660,11 @@ func (s *RetryLayerUserStore) GetTeamGroupUsers(teamID string) ([]*model.User, e
 
 }
 
-func (s *RetryLayerUserStore) GetUnreadCount(userID string) (int64, error) {
+func (s *RetryLayerUserStore) GetUnreadCount(userID string, isCRTEnabled bool) (int64, error) {
 
 	tries := 0
 	for {
-		result, err := s.UserStore.GetUnreadCount(userID)
+		result, err := s.UserStore.GetUnreadCount(userID, isCRTEnabled)
 		if err == nil {
 			return result, nil
 		}
diff --git a/store/sqlstore/user_store.go b/store/sqlstore/user_store.go
index 8a359ed870..201aac0ca3 100644
--- a/store/sqlstore/user_store.go
+++ b/store/sqlstore/user_store.go
@@ -1371,9 +1371,18 @@ func (us SqlUserStore) AnalyticsActiveCountForPeriod(startTime int64, endTime in
 	return v, nil
 }
 
-func (us SqlUserStore) GetUnreadCount(userId string) (int64, error) {
+func (us SqlUserStore) GetUnreadCount(userId string, isCRTEnabled bool) (int64, error) {
+	var totalMsgCountColumn = "c.TotalMsgCount"
+	var msgCountColumn = "cm.MsgCount"
+	var mentionCountColumn = "cm.MentionCount"
+	if isCRTEnabled {
+		totalMsgCountColumn = "c.TotalMsgCountRoot"
+		msgCountColumn = "cm.MsgCountRoot"
+		mentionCountColumn = "cm.MentionCountRoot"
+	}
+
 	query := `
-		SELECT SUM(CASE WHEN c.Type = ? THEN (c.TotalMsgCount - cm.MsgCount) ELSE cm.MentionCount END)
+		SELECT SUM(CASE WHEN c.Type = ? THEN (` + totalMsgCountColumn + ` - ` + msgCountColumn + `) ELSE ` + mentionCountColumn + ` END)
 		FROM Channels c
 		INNER JOIN ChannelMembers cm
 			ON cm.ChannelId = c.Id
diff --git a/store/store.go b/store/store.go
index 0e392bf861..df2473b701 100644
--- a/store/store.go
+++ b/store/store.go
@@ -447,7 +447,7 @@ type UserStore interface {
 	PermanentDelete(userID string) error
 	AnalyticsActiveCount(timestamp int64, options model.UserCountOptions) (int64, error)
 	AnalyticsActiveCountForPeriod(startTime int64, endTime int64, options model.UserCountOptions) (int64, error)
-	GetUnreadCount(userID string) (int64, error)
+	GetUnreadCount(userID string, isCRTEnabled bool) (int64, error)
 	GetUnreadCountForChannel(userID string, channelID string) (int64, error)
 	GetAnyUnreadPostCountForChannel(userID string, channelID string) (int64, error)
 	GetRecentlyActiveUsersForTeam(teamID string, offset, limit int, viewRestrictions *model.ViewUsersRestrictions) ([]*model.User, error)
diff --git a/store/storetest/mocks/UserStore.go b/store/storetest/mocks/UserStore.go
index afb1ae0c9a..ea0fdcfcc0 100644
--- a/store/storetest/mocks/UserStore.go
+++ b/store/storetest/mocks/UserStore.go
@@ -960,20 +960,20 @@ func (_m *UserStore) GetTeamGroupUsers(teamID string) ([]*model.User, error) {
 	return r0, r1
 }
 
-// GetUnreadCount provides a mock function with given fields: userID
-func (_m *UserStore) GetUnreadCount(userID string) (int64, error) {
-	ret := _m.Called(userID)
+// GetUnreadCount provides a mock function with given fields: userID, isCRTEnabled
+func (_m *UserStore) GetUnreadCount(userID string, isCRTEnabled bool) (int64, error) {
+	ret := _m.Called(userID, isCRTEnabled)
 
 	var r0 int64
-	if rf, ok := ret.Get(0).(func(string) int64); ok {
-		r0 = rf(userID)
+	if rf, ok := ret.Get(0).(func(string, bool) int64); ok {
+		r0 = rf(userID, isCRTEnabled)
 	} else {
 		r0 = ret.Get(0).(int64)
 	}
 
 	var r1 error
-	if rf, ok := ret.Get(1).(func(string) error); ok {
-		r1 = rf(userID)
+	if rf, ok := ret.Get(1).(func(string, bool) error); ok {
+		r1 = rf(userID, isCRTEnabled)
 	} else {
 		r1 = ret.Error(1)
 	}
diff --git a/store/storetest/user_store.go b/store/storetest/user_store.go
index cef2ce02e8..fd2d8746d9 100644
--- a/store/storetest/user_store.go
+++ b/store/storetest/user_store.go
@@ -2440,14 +2440,23 @@ func testUserUnreadCount(t *testing.T, ss store.Store) {
 	nErr = ss.Channel().IncrementMentionCount(c2.Id, []string{u2.Id}, false)
 	require.NoError(t, nErr)
 
-	badge, unreadCountErr := ss.User().GetUnreadCount(u2.Id)
+	badge, unreadCountErr := ss.User().GetUnreadCount(u2.Id, false)
 	require.NoError(t, unreadCountErr)
 	require.Equal(t, int64(3), badge, "should have 3 unread messages")
 
-	badge, unreadCountErr = ss.User().GetUnreadCount(u3.Id)
+	badge, unreadCountErr = ss.User().GetUnreadCount(u3.Id, false)
 	require.NoError(t, unreadCountErr)
 	require.Equal(t, int64(1), badge, "should have 1 unread message")
 
+	// Increment root mentions by 1
+	nErr = ss.Channel().IncrementMentionCount(c1.Id, []string{u3.Id}, true)
+	require.NoError(t, nErr)
+
+	// CRT is enabled, only root mentions are counted
+	badge, unreadCountErr = ss.User().GetUnreadCount(u3.Id, true)
+	require.NoError(t, unreadCountErr)
+	require.Equal(t, int64(1), badge, "should have 1 unread message with CRT")
+
 	badge, unreadCountErr = ss.User().GetUnreadCountForChannel(u2.Id, c1.Id)
 	require.NoError(t, unreadCountErr)
 	require.Equal(t, int64(1), badge, "should have 1 unread messages for that channel")
diff --git a/store/timerlayer/timerlayer.go b/store/timerlayer/timerlayer.go
index 6835edbb68..3a4e40ed39 100644
--- a/store/timerlayer/timerlayer.go
+++ b/store/timerlayer/timerlayer.go
@@ -9983,10 +9983,10 @@ func (s *TimerLayerUserStore) GetTeamGroupUsers(teamID string) ([]*model.User, e
 	return result, err
 }
 
-func (s *TimerLayerUserStore) GetUnreadCount(userID string) (int64, error) {
+func (s *TimerLayerUserStore) GetUnreadCount(userID string, isCRTEnabled bool) (int64, error) {
 	start := time.Now()
 
-	result, err := s.UserStore.GetUnreadCount(userID)
+	result, err := s.UserStore.GetUnreadCount(userID, isCRTEnabled)
 
 	elapsed := float64(time.Since(start)) / float64(time.Second)
 	if s.Root.Metrics != nil {