diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07327dab21..9d3827e883 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## master / unreleased
 
+* [ENHANCEMENT] Ruler: Add new ruler metric `cortex_ruler_rule_groups_in_store` that is the total rule groups per tenant in store, which can be used to compare with `cortex_prometheus_rule_group_rules` to count the number of rule groups that are not loaded by a ruler. #5869
 
 ## 1.18.0 in progress
 
diff --git a/integration/ruler_test.go b/integration/ruler_test.go
index c05fd2ceb4..d56bb696aa 100644
--- a/integration/ruler_test.go
+++ b/integration/ruler_test.go
@@ -267,6 +267,9 @@ func TestRulerSharding(t *testing.T) {
 	// between the two rulers.
 	require.NoError(t, ruler1.WaitSumMetrics(e2e.Less(numRulesGroups), "cortex_prometheus_rule_group_rules"))
 	require.NoError(t, ruler2.WaitSumMetrics(e2e.Less(numRulesGroups), "cortex_prometheus_rule_group_rules"))
+	// Even with rules sharded, we expect rulers to have the same cortex_ruler_rule_groups_in_store metric values
+	require.NoError(t, ruler1.WaitSumMetrics(e2e.Equals(numRulesGroups), "cortex_ruler_rule_groups_in_store"))
+	require.NoError(t, ruler2.WaitSumMetrics(e2e.Equals(numRulesGroups), "cortex_ruler_rule_groups_in_store"))
 
 	// Fetch the rules and ensure they match the configured ones.
 	actualGroups, err := c.GetPrometheusRules(e2ecortex.DefaultFilter)
diff --git a/pkg/ruler/manager_metrics.go b/pkg/ruler/manager_metrics.go
index 130387407c..ef211ddd89 100644
--- a/pkg/ruler/manager_metrics.go
+++ b/pkg/ruler/manager_metrics.go
@@ -271,3 +271,39 @@ func (m *RuleEvalMetrics) deletePerUserMetrics(userID string) {
 		m.RulerQuerySeconds.DeleteLabelValues(userID)
 	}
 }
+
+type RuleGroupMetrics struct {
+	RuleGroupsInStore *prometheus.GaugeVec
+	tenants           map[string]struct{}
+	allowedTenants    *util.AllowedTenants
+}
+
+func NewRuleGroupMetrics(reg prometheus.Registerer, allowedTenants *util.AllowedTenants) *RuleGroupMetrics {
+	m := &RuleGroupMetrics{
+		RuleGroupsInStore: promauto.With(reg).NewGaugeVec(prometheus.GaugeOpts{
+			Name: "cortex_ruler_rule_groups_in_store",
+			Help: "The number of rule groups a tenant has in store.",
+		}, []string{"user"}),
+		allowedTenants: allowedTenants,
+	}
+	return m
+}
+
+// UpdateRuleGroupsInStore updates the cortex_ruler_rule_groups_in_store metric with the provided number of rule
+// groups per tenant and removing the metrics for tenants that are not present anymore
+func (r *RuleGroupMetrics) UpdateRuleGroupsInStore(ruleGroupsCount map[string]int) {
+	tenants := make(map[string]struct{}, len(ruleGroupsCount))
+	for userID, count := range ruleGroupsCount {
+		if !r.allowedTenants.IsAllowed(userID) { // if the tenant is disabled just ignore its rule groups
+			continue
+		}
+		tenants[userID] = struct{}{}
+		r.RuleGroupsInStore.WithLabelValues(userID).Set(float64(count))
+	}
+	for userID := range r.tenants {
+		if _, ok := tenants[userID]; !ok {
+			r.RuleGroupsInStore.DeleteLabelValues(userID)
+		}
+	}
+	r.tenants = tenants
+}
diff --git a/pkg/ruler/manager_metrics_test.go b/pkg/ruler/manager_metrics_test.go
index 4b851ef192..60b68452ca 100644
--- a/pkg/ruler/manager_metrics_test.go
+++ b/pkg/ruler/manager_metrics_test.go
@@ -595,3 +595,41 @@ func TestRuleEvalMetricsDeletePerUserMetrics(t *testing.T) {
 		require.Contains(t, mfm[name].String(), "value:\"fake2\"")
 	}
 }
+
+func TestRuleGroupMetrics(t *testing.T) {
+	reg := prometheus.NewPedanticRegistry()
+	m := NewRuleGroupMetrics(reg, util.NewAllowedTenants(nil, []string{"fake3"}))
+	m.UpdateRuleGroupsInStore(map[string]int{
+		"fake1": 10,
+		"fake2": 20,
+		"fake3": 30,
+	})
+	gm, err := reg.Gather()
+	require.NoError(t, err)
+	mfm, err := util.NewMetricFamilyMap(gm)
+	require.NoError(t, err)
+	require.Equal(t, 2, len(mfm["cortex_ruler_rule_groups_in_store"].Metric))
+	requireMetricEqual(t, mfm["cortex_ruler_rule_groups_in_store"].Metric[0], map[string]string{
+		"user": "fake1",
+	}, float64(10))
+	requireMetricEqual(t, mfm["cortex_ruler_rule_groups_in_store"].Metric[1], map[string]string{
+		"user": "fake2",
+	}, float64(20))
+	m.UpdateRuleGroupsInStore(map[string]int{
+		"fake2": 30,
+	})
+	gm, err = reg.Gather()
+	require.NoError(t, err)
+	mfm, err = util.NewMetricFamilyMap(gm)
+	require.NoError(t, err)
+	require.Equal(t, 1, len(mfm["cortex_ruler_rule_groups_in_store"].Metric))
+	requireMetricEqual(t, mfm["cortex_ruler_rule_groups_in_store"].Metric[0], map[string]string{
+		"user": "fake2",
+	}, float64(30))
+	m.UpdateRuleGroupsInStore(make(map[string]int))
+	gm, err = reg.Gather()
+	require.NoError(t, err)
+	mfm, err = util.NewMetricFamilyMap(gm)
+	require.NoError(t, err)
+	require.Nil(t, mfm["cortex_ruler_rule_groups_in_store"])
+}
diff --git a/pkg/ruler/ruler.go b/pkg/ruler/ruler.go
index d47e4320c8..4f121570cc 100644
--- a/pkg/ruler/ruler.go
+++ b/pkg/ruler/ruler.go
@@ -294,6 +294,7 @@ type Ruler struct {
 	ruleGroupStoreLoadDuration prometheus.Gauge
 	ruleGroupSyncDuration      prometheus.Gauge
 	rulerGetRulesFailures      *prometheus.CounterVec
+	ruleGroupMetrics           *RuleGroupMetrics
 
 	allowedTenants *util.AllowedTenants
 
@@ -342,6 +343,7 @@ func newRuler(cfg Config, manager MultiTenantManager, reg prometheus.Registerer,
 			Help: "The total number of failed rules request sent to rulers in getShardedRules.",
 		}, []string{"ruler"}),
 	}
+	ruler.ruleGroupMetrics = NewRuleGroupMetrics(reg, ruler.allowedTenants)
 
 	if len(cfg.EnabledTenants) > 0 {
 		level.Info(ruler.logger).Log("msg", "ruler using enabled users", "enabled", strings.Join(cfg.EnabledTenants, ", "))
@@ -667,7 +669,9 @@ func (r *Ruler) listRulesNoSharding(ctx context.Context) (map[string]rulespb.Rul
 	if err != nil {
 		return nil, nil, err
 	}
+	ruleGroupCounts := make(map[string]int, len(allRuleGroups))
 	for userID, groups := range allRuleGroups {
+		ruleGroupCounts[userID] = len(groups)
 		disabledRuleGroupsForUser := r.limits.DisabledRuleGroups(userID)
 		if len(disabledRuleGroupsForUser) == 0 {
 			continue
@@ -682,6 +686,7 @@ func (r *Ruler) listRulesNoSharding(ctx context.Context) (map[string]rulespb.Rul
 		}
 		allRuleGroups[userID] = filteredGroupsForUser
 	}
+	r.ruleGroupMetrics.UpdateRuleGroupsInStore(ruleGroupCounts)
 	return allRuleGroups, nil, nil
 }
 
@@ -691,9 +696,11 @@ func (r *Ruler) listRulesShardingDefault(ctx context.Context) (map[string]rulesp
 		return nil, nil, err
 	}
 
+	ruleGroupCounts := make(map[string]int, len(configs))
 	ownedConfigs := make(map[string]rulespb.RuleGroupList)
 	backedUpConfigs := make(map[string]rulespb.RuleGroupList)
 	for userID, groups := range configs {
+		ruleGroupCounts[userID] = len(groups)
 		owned := filterRuleGroups(userID, groups, r.limits.DisabledRuleGroups(userID), r.ring, r.lifecycler.GetInstanceAddr(), r.logger, r.ringCheckErrors)
 		if len(owned) > 0 {
 			ownedConfigs[userID] = owned
@@ -705,6 +712,7 @@ func (r *Ruler) listRulesShardingDefault(ctx context.Context) (map[string]rulesp
 			}
 		}
 	}
+	r.ruleGroupMetrics.UpdateRuleGroupsInStore(ruleGroupCounts)
 	return ownedConfigs, backedUpConfigs, nil
 }
 
@@ -732,6 +740,7 @@ func (r *Ruler) listRulesShuffleSharding(ctx context.Context) (map[string]rulesp
 	}
 
 	if len(userRings) == 0 {
+		r.ruleGroupMetrics.UpdateRuleGroupsInStore(make(map[string]int))
 		return nil, nil, nil
 	}
 
@@ -744,6 +753,8 @@ func (r *Ruler) listRulesShuffleSharding(ctx context.Context) (map[string]rulesp
 	mu := sync.Mutex{}
 	owned := map[string]rulespb.RuleGroupList{}
 	backedUp := map[string]rulespb.RuleGroupList{}
+	gLock := sync.Mutex{}
+	ruleGroupCounts := make(map[string]int, len(userRings))
 
 	concurrency := loadRulesConcurrency
 	if len(userRings) < concurrency {
@@ -758,6 +769,9 @@ func (r *Ruler) listRulesShuffleSharding(ctx context.Context) (map[string]rulesp
 				if err != nil {
 					return errors.Wrapf(err, "failed to fetch rule groups for user %s", userID)
 				}
+				gLock.Lock()
+				ruleGroupCounts[userID] = len(groups)
+				gLock.Unlock()
 
 				filterOwned := filterRuleGroups(userID, groups, r.limits.DisabledRuleGroups(userID), userRings[userID], r.lifecycler.GetInstanceAddr(), r.logger, r.ringCheckErrors)
 				var filterBackup []*rulespb.RuleGroupDesc
@@ -781,6 +795,7 @@ func (r *Ruler) listRulesShuffleSharding(ctx context.Context) (map[string]rulesp
 	}
 
 	err = g.Wait()
+	r.ruleGroupMetrics.UpdateRuleGroupsInStore(ruleGroupCounts)
 	return owned, backedUp, err
 }
 
diff --git a/pkg/ruler/ruler_test.go b/pkg/ruler/ruler_test.go
index c0d9e43804..af338443ca 100644
--- a/pkg/ruler/ruler_test.go
+++ b/pkg/ruler/ruler_test.go
@@ -247,10 +247,23 @@ func buildRuler(t *testing.T, rulerConfig Config, querierTestConfig *querier.Tes
 func newTestRuler(t *testing.T, rulerConfig Config, store rulestore.RuleStore, querierTestConfig *querier.TestConfig) *Ruler {
 	ruler, _ := buildRuler(t, rulerConfig, querierTestConfig, store, nil)
 	require.NoError(t, services.StartAndAwaitRunning(context.Background(), ruler))
+	rgs, err := store.ListAllRuleGroups(context.Background())
+	require.NoError(t, err)
 
-	// Ensure all rules are loaded before usage
-	ruler.syncRules(context.Background(), rulerSyncReasonInitial)
-
+	// Wait to ensure syncRules has finished and all rules are loaded before usage
+	deadline := time.Now().Add(3 * time.Second)
+	for {
+		loaded := true
+		for tenantId := range rgs {
+			if len(ruler.manager.GetRules(tenantId)) == 0 {
+				loaded = false
+			}
+		}
+		if time.Now().After(deadline) || loaded {
+			break
+		}
+		time.Sleep(50 * time.Millisecond)
+	}
 	return ruler
 }