diff --git a/cmd/tsdb/main.go b/cmd/tsdb/main.go
index 0278c14c5..c7e85204b 100644
--- a/cmd/tsdb/main.go
+++ b/cmd/tsdb/main.go
@@ -130,7 +130,7 @@ func (b *writeBenchmark) run() {
 
 	dur := measureTime("ingestScrapes", func() {
 		b.startProfiling()
-		total, err = b.ingestScrapes(metrics, 2000)
+		total, err = b.ingestScrapes(metrics, 3000)
 		if err != nil {
 			exitWithError(err)
 		}
diff --git a/db.go b/db.go
index aca7249df..3622a77f5 100644
--- a/db.go
+++ b/db.go
@@ -378,36 +378,9 @@ func (db *DB) compact() (changes bool, err error) {
 			return changes, errors.Wrapf(err, "compact %s", plan)
 		}
 		changes = true
-
-		// close blocks in plan so that we can remove files.
-		var blocks []*Block
-		db.mtx.Lock()
-		oldBlocks := db.blocks
-		for _, b := range oldBlocks {
-			keep := true
-			for _, pd := range plan {
-				if pd == b.Dir() {
-					keep = false
-					break
-				}
-			}
-			if keep {
-				blocks = append(blocks, b)
-			} else {
-				b.Close()
-			}
-		}
-		db.blocks = blocks
-		db.mtx.Unlock()
-
-		for _, pd := range plan {
-			if err := os.RemoveAll(pd); err != nil {
-				return changes, errors.Wrap(err, "delete compacted block")
-			}
-		}
 		runtime.GC()
 
-		if err := db.reload(); err != nil {
+		if err := db.reload(plan...); err != nil {
 			return changes, errors.Wrap(err, "reload blocks")
 		}
 		runtime.GC()
@@ -461,7 +434,18 @@ func (db *DB) getBlock(id ulid.ULID) (*Block, bool) {
 	return nil, false
 }
 
-func (db *DB) reload() (err error) {
+func stringsContain(set []string, elem string) bool {
+	for _, e := range set {
+		if elem == e {
+			return true
+		}
+	}
+	return false
+}
+
+// reload on-disk blocks and trigger head truncation if new blocks appeared. It takes
+// a list of block directories which should be deleted during reload.
+func (db *DB) reload(deleteable ...string) (err error) {
 	defer func() {
 		if err != nil {
 			db.metrics.reloadsFailed.Inc()
@@ -483,6 +467,10 @@ func (db *DB) reload() (err error) {
 		if err != nil {
 			return errors.Wrapf(err, "read meta information %s", dir)
 		}
+		// If the block is pending for deletion, don't add it to the new block set.
+		if stringsContain(deleteable, dir) {
+			continue
+		}
 
 		b, ok := db.getBlock(meta.ULID)
 		if !ok {
@@ -508,8 +496,14 @@ func (db *DB) reload() (err error) {
 	db.mtx.Unlock()
 
 	for _, b := range oldBlocks {
-		if _, ok := exist[b.Meta().ULID]; !ok {
-			b.Close()
+		if _, ok := exist[b.Meta().ULID]; ok {
+			continue
+		}
+		if err := b.Close(); err != nil {
+			level.Warn(db.logger).Log("msg", "closing block failed", "err", err)
+		}
+		if err := os.RemoveAll(b.Dir()); err != nil {
+			level.Warn(db.logger).Log("msg", "deleting block failed", "err", err)
 		}
 	}