diff --git a/cmd/prometheus/config.go b/cmd/prometheus/config.go
index 1c5e7679a..839b3f4ce 100644
--- a/cmd/prometheus/config.go
+++ b/cmd/prometheus/config.go
@@ -113,7 +113,7 @@ func init() {
 		"How long to retain samples in the local storage.",
 	)
 	cfg.fs.IntVar(
-		&cfg.storage.MaxChunksToPersist, "storage.local.max-chunks-to-persist", 1024*1024,
+		&cfg.storage.MaxChunksToPersist, "storage.local.max-chunks-to-persist", 512*1024,
 		"How many chunks can be waiting for persistence before sample ingestion will stop. Many chunks waiting to be persisted will increase the checkpoint size.",
 	)
 	cfg.fs.DurationVar(
diff --git a/storage/local/persistence.go b/storage/local/persistence.go
index 96a478a04..72b989ccb 100644
--- a/storage/local/persistence.go
+++ b/storage/local/persistence.go
@@ -861,6 +861,12 @@ func (p *persistence) loadSeriesMapAndHeads() (sm *seriesMap, chunksToPersist in
 			}
 		}
 
+		headChunkClosed := persistWatermark >= numChunkDescs
+		if !headChunkClosed {
+			// Head chunk is not ready for persisting yet.
+			chunksToPersist--
+		}
+
 		fingerprintToSeries[model.Fingerprint(fp)] = &memorySeries{
 			metric:           model.Metric(metric),
 			chunkDescs:       chunkDescs,
@@ -869,7 +875,7 @@ func (p *persistence) loadSeriesMapAndHeads() (sm *seriesMap, chunksToPersist in
 			chunkDescsOffset: int(chunkDescsOffset),
 			savedFirstTime:   model.Time(savedFirstTime),
 			lastTime:         chunkDescs[len(chunkDescs)-1].lastTime(),
-			headChunkClosed:  persistWatermark >= numChunkDescs,
+			headChunkClosed:  headChunkClosed,
 		}
 	}
 	return sm, chunksToPersist, nil