diff --git a/pkg/bloombuild/planner/queue/queue.go b/pkg/bloombuild/planner/queue/queue.go
index b36be563068..68c8283ddcc 100644
--- a/pkg/bloombuild/planner/queue/queue.go
+++ b/pkg/bloombuild/planner/queue/queue.go
@@ -57,6 +57,17 @@ func NewQueue(
 	limits Limits,
 	metrics *Metrics,
 	storeMetrics storage.ClientMetrics,
+) (*Queue, error) {
+	return newQueue(logger, cfg, limits, metrics, storeMetrics, 5*time.Minute, 1*time.Hour)
+}
+
+func newQueue(
+	logger log.Logger,
+	cfg Config,
+	limits Limits,
+	metrics *Metrics,
+	storeMetrics storage.ClientMetrics,
+	activeUsersCleanupInterval, activeUsersInactiveTimeout time.Duration,
 ) (*Queue, error) {
 	// Configure the filesystem client if we are storing tasks on disk.
 	var diskClient client.ObjectClient
@@ -73,8 +84,15 @@ func NewQueue(
 
 	tasksQueue := queue.NewRequestQueue(cfg.MaxQueuedTasksPerTenant, 0, limits, metrics)
 
-	// Clean metrics for inactive users: do not have added tasks to the queue in the last 1 hour
-	activeUsers := util.NewActiveUsersCleanupService(5*time.Minute, 1*time.Hour, func(user string) {
+	// Re-register the user when the queue is non-empty: PurgeInactiveUsers has already
+	// removed it from its tracking map by the time this callback runs, so without this
+	// the metrics would never be cleaned up once the backlog drains.
+	var activeUsers *util.ActiveUsersCleanupService
+	activeUsers = util.NewActiveUsersCleanupService(activeUsersCleanupInterval, activeUsersInactiveTimeout, func(user string) {
+		if tasksQueue.GetUserQueueLength(user) > 0 {
+			activeUsers.UpdateUserTimestamp(user, time.Now())
+			return
+		}
 		metrics.Cleanup(user)
 	})
 
diff --git a/pkg/bloombuild/planner/queue/queue_test.go b/pkg/bloombuild/planner/queue/queue_test.go
index 9947ac9381a..13d613ace7d 100644
--- a/pkg/bloombuild/planner/queue/queue_test.go
+++ b/pkg/bloombuild/planner/queue/queue_test.go
@@ -5,11 +5,14 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
+	"time"
 
 	"github.com/go-kit/log"
 	"github.com/grafana/dskit/services"
 	"github.com/prometheus/client_golang/prometheus"
+	"github.com/prometheus/client_golang/prometheus/testutil"
 	"github.com/prometheus/common/model"
 	"github.com/stretchr/testify/require"
 
@@ -209,3 +212,54 @@ type fakeLimits struct{}
 func (f fakeLimits) MaxConsumers(_ string, _ int) int {
 	return 0 // Unlimited
 }
+
+func TestActiveUsersCleanupSkippedWhileQueueNotEmpty(t *testing.T) {
+	const (
+		cleanupInterval = 10 * time.Millisecond
+		inactiveTimeout = 50 * time.Millisecond
+		numTasks        = 5
+	)
+
+	reg := prometheus.NewPedanticRegistry()
+	queueMetrics := NewMetrics(reg, "test", "queue")
+	clientMetrics := storage.NewClientMetrics()
+	defer clientMetrics.Unregister()
+
+	cfg := Config{MaxQueuedTasksPerTenant: 1000}
+	q, err := newQueue(log.NewNopLogger(), cfg, fakeLimits{}, queueMetrics, clientMetrics, cleanupInterval, inactiveTimeout)
+	require.NoError(t, err)
+
+	require.NoError(t, services.StartAndAwaitRunning(context.Background(), q))
+	t.Cleanup(func() { _ = services.StopAndAwaitTerminated(context.Background(), q) })
+
+	const consumer = "fakeConsumer"
+	q.RegisterConsumerConnection(consumer)
+	defer q.UnregisterConsumerConnection(consumer)
+
+	tasks := createTasks(numTasks)
+	for _, task := range tasks {
+		require.NoError(t, q.Enqueue(task.ProtoTask, task.taskMeta, nil))
+	}
+
+	time.Sleep(3 * inactiveTimeout)
+
+	expected := fmt.Sprintf(`# HELP test_queue_queue_length Number of queries in the queue.
+# TYPE test_queue_queue_length gauge
+test_queue_queue_length{user="fakeTenant"} %d
+`, numTasks)
+	require.NoError(t, testutil.GatherAndCompare(reg, strings.NewReader(expected), "test_queue_queue_length"))
+
+	idx := StartIndex
+	for i := 0; i < numTasks; i++ {
+		var task *protos.ProtoTask
+		task, _, idx, err = q.Dequeue(context.Background(), idx, consumer)
+		require.NoError(t, err)
+		require.NotNil(t, task)
+		q.Release(task)
+	}
+
+	require.Eventually(t, func() bool {
+		count, err := testutil.GatherAndCount(reg, "test_queue_queue_length")
+		return err == nil && count == 0
+	}, 5*inactiveTimeout, cleanupInterval, "queue_length series should be cleaned up after drain")
+}
diff --git a/pkg/queue/queue.go b/pkg/queue/queue.go
index 7a5f18c1c90..e98669e6e77 100644
--- a/pkg/queue/queue.go
+++ b/pkg/queue/queue.go
@@ -299,6 +299,16 @@ func (q *RequestQueue) GetConnectedConsumersMetric() float64 {
 	return float64(q.connectedConsumers.Load())
 }
 
+// GetUserQueueLength returns the number of pending requests for the given tenant.
+func (q *RequestQueue) GetUserQueueLength(tenant string) int {
+	q.mtx.Lock()
+	defer q.mtx.Unlock()
+	if ptr, ok := q.queues.perUserQueueLen[tenant]; ok {
+		return *ptr
+	}
+	return 0
+}
+
 // contextCond is a *sync.Cond with Wait() method overridden to support context-based waiting.
 type contextCond struct {
 	*sync.Cond