diff --git a/lib/streamaggr/streamaggr.go b/lib/streamaggr/streamaggr.go
index d975f9406..730c9897b 100644
--- a/lib/streamaggr/streamaggr.go
+++ b/lib/streamaggr/streamaggr.go
@@ -82,16 +82,22 @@ type Options struct {
 	// The last sample per each series is left per each DedupInterval if DedupInterval > 0.
 	//
 	// By default deduplication is disabled.
+	//
+	// The deduplication can be set up individually per each aggregation via dedup_interval option.
 	DedupInterval time.Duration
 
 	// NoAlignFlushToInterval disables alignment of flushes to the aggregation interval.
 	//
 	// By default flushes are aligned to aggregation interval.
+	//
+	// The alignment of flushes can be disabled individually per each aggregation via no_align_flush_to_interval option.
 	NoAlignFlushToInterval bool
 
-	// FlushOnShutdown enables flush of incomplete state on shutdown.
+	// FlushOnShutdown enables flush of incomplete state on start and shutdown.
 	//
 	// By default incomplete state is dropped on shutdown.
+	//
+	// The flush of incomplete state can be enabled individually per each aggregation via flush_on_shutdown option.
 	FlushOnShutdown bool
 
 	// KeepMetricNames instructs to leave metric names as is for the output time series without adding any suffix.
@@ -100,6 +106,7 @@ type Options struct {
 	//
 	//     input_name:<interval>[_by_<by_labels>][_without_<without_labels>]_<output>
 	//
+	// This option can be overriden individually per each aggregation via keep_metric_names option.
 	KeepMetricNames bool
 }
 
@@ -601,20 +608,22 @@ func (a *aggregator) runFlusher(pushFunc PushFunc, alignFlushToInterval, skipInc
 		if d < interval {
 			sleep(d)
 		}
-		flushTickerCh <- time.NewTicker(interval)
+		t := time.NewTicker(interval)
+		if skipIncompleteFlush {
+			a.dedupFlush(dedupInterval)
+			a.flush(nil, interval)
+		}
+		flushTickerCh <- t
 	}()
 
 	var flushTickerC <-chan time.Time
 	var dedupFlushTickerC <-chan time.Time
-	isFirstFlush := true
 	for {
 		select {
 		case <-a.stopCh:
 			if !skipIncompleteFlush {
-				if dedupInterval > 0 {
-					a.dedupFlush()
-				}
-				a.flush(pushFunc)
+				a.dedupFlush(dedupInterval)
+				a.flush(pushFunc, interval)
 			}
 			return
 		case flushTicker := <-flushTickerCh:
@@ -624,43 +633,42 @@ func (a *aggregator) runFlusher(pushFunc PushFunc, alignFlushToInterval, skipInc
 			dedupFlushTickerC = dedupFlushTicker.C
 			defer dedupFlushTicker.Stop()
 		case <-flushTickerC:
-			if isFirstFlush {
-				isFirstFlush = false
-				if alignFlushToInterval && skipIncompleteFlush {
-					a.flush(nil)
-					continue
-				}
-			}
-			startTime := time.Now()
-			a.flush(pushFunc)
-			d := time.Since(startTime)
-			a.flushDuration.Update(d.Seconds())
-			if d > interval {
-				a.flushTimeouts.Inc()
-				logger.Warnf("stream aggregation couldn't be finished in the configured interval=%s; it took %s; "+
-					"possible solutions: increase interval; use match filter matching smaller number of series; "+
-					"reduce samples' ingestion rate to stream aggregation", interval, d)
+			select {
+			case <-dedupFlushTickerC:
+				// flush deduplicated samples if needed before flushing the aggregated samples
+				a.dedupFlush(dedupInterval)
+			default:
 			}
+			a.flush(pushFunc, interval)
 		case <-dedupFlushTickerC:
-			startTime := time.Now()
-			a.dedupFlush()
-			d := time.Since(startTime)
-			a.dedupFlushDuration.Update(d.Seconds())
-			if d > dedupInterval {
-				a.dedupFlushTimeouts.Inc()
-				logger.Warnf("stream aggregation deduplication couldn't be finished in the configured dedup_interval=%s; it took %s; "+
-					"possible solutions: increase dedup_interval; use match filter matching smaller number of series; "+
-					"reduce samples' ingestion rate to stream aggregation", dedupInterval, d)
-			}
+			a.dedupFlush(dedupInterval)
 		}
 	}
 }
 
-func (a *aggregator) dedupFlush() {
+func (a *aggregator) dedupFlush(dedupInterval time.Duration) {
+	if dedupInterval <= 0 {
+		// The de-duplication is disabled.
+		return
+	}
+
+	startTime := time.Now()
+
 	a.da.flush(a.pushSamples)
+
+	d := time.Since(startTime)
+	a.dedupFlushDuration.Update(d.Seconds())
+	if d > dedupInterval {
+		a.dedupFlushTimeouts.Inc()
+		logger.Warnf("deduplication couldn't be finished in the configured dedup_interval=%s; it took %.03f; "+
+			"possible solutions: increase dedup_interval; use match filter matching smaller number of series; "+
+			"reduce samples' ingestion rate to stream aggregation", dedupInterval, d.Seconds())
+	}
 }
 
-func (a *aggregator) flush(pushFunc PushFunc) {
+func (a *aggregator) flush(pushFunc PushFunc, interval time.Duration) {
+	startTime := time.Now()
+
 	var wg sync.WaitGroup
 	for _, as := range a.aggrStates {
 		flushConcurrencyCh <- struct{}{}
@@ -679,6 +687,15 @@ func (a *aggregator) flush(pushFunc PushFunc) {
 		}(as)
 	}
 	wg.Wait()
+
+	d := time.Since(startTime)
+	a.flushDuration.Update(d.Seconds())
+	if d > interval {
+		a.flushTimeouts.Inc()
+		logger.Warnf("stream aggregation couldn't be finished in the configured interval=%s; it took %.03f; "+
+			"possible solutions: increase interval; use match filter matching smaller number of series; "+
+			"reduce samples' ingestion rate to stream aggregation", interval, d.Seconds())
+	}
 }
 
 var flushConcurrencyCh = make(chan struct{}, cgroup.AvailableCPUs())
diff --git a/lib/streamaggr/streamaggr_timing_test.go b/lib/streamaggr/streamaggr_timing_test.go
index ad220eee6..ed6c8f032 100644
--- a/lib/streamaggr/streamaggr_timing_test.go
+++ b/lib/streamaggr/streamaggr_timing_test.go
@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/prompbmarshal"
 )
@@ -55,7 +56,7 @@ func benchmarkAggregatorsFlushSerial(b *testing.B, output string) {
 	for i := 0; i < b.N; i++ {
 		matchIdxs = a.Push(benchSeries, matchIdxs)
 		for _, aggr := range a.as {
-			aggr.flush(pushFunc)
+			aggr.flush(pushFunc, time.Hour)
 		}
 	}
 }