diff --git a/tsdb/series_file_test.go b/tsdb/series_file_test.go
index 7ace89add1..25e575ce20 100644
--- a/tsdb/series_file_test.go
+++ b/tsdb/series_file_test.go
@@ -169,6 +169,54 @@ func TestSeriesFile_Type(t *testing.T) {
 	}
 }
 
+// Ensure series file deletions persist across compactions.
+func TestSeriesFile_DeleteSeriesID(t *testing.T) {
+	sfile := MustOpenSeriesFile()
+	defer sfile.Close()
+
+	if err := sfile.CreateSeriesListIfNotExists(&tsdb.SeriesCollection{
+		Names: [][]byte{[]byte("m1")},
+		Tags:  []models.Tags{{}},
+		Types: []models.FieldType{models.String},
+	}); err != nil {
+		t.Fatal(err)
+	} else if err := sfile.CreateSeriesListIfNotExists(&tsdb.SeriesCollection{
+		Names: [][]byte{[]byte("m2")},
+		Tags:  []models.Tags{{}},
+		Types: []models.FieldType{models.String},
+	}); err != nil {
+		t.Fatal(err)
+	} else if err := sfile.ForceCompact(); err != nil {
+		t.Fatal(err)
+	}
+	id := sfile.SeriesID([]byte("m1"), nil, nil)
+
+	// Delete and ensure deletion.
+	if err := sfile.DeleteSeriesID(id); err != nil {
+		t.Fatal(err)
+	} else if err := sfile.CreateSeriesListIfNotExists(&tsdb.SeriesCollection{
+		Names: [][]byte{[]byte("m1")},
+		Tags:  []models.Tags{{}},
+		Types: []models.FieldType{models.String},
+	}); err != nil {
+		t.Fatal(err)
+	} else if !sfile.IsDeleted(id) {
+		t.Fatal("expected deletion before compaction")
+	}
+
+	if err := sfile.ForceCompact(); err != nil {
+		t.Fatal(err)
+	} else if !sfile.IsDeleted(id) {
+		t.Fatal("expected deletion after compaction")
+	}
+
+	if err := sfile.Reopen(); err != nil {
+		t.Fatal(err)
+	} else if !sfile.IsDeleted(id) {
+		t.Fatal("expected deletion after reopen")
+	}
+}
+
 // Series represents name/tagset pairs that are used in testing.
 type Series struct {
 	Name    []byte
@@ -206,3 +254,22 @@ func (f *SeriesFile) Close() error {
 	defer os.RemoveAll(f.Path())
 	return f.SeriesFile.Close()
 }
+
+// Reopen close & reopens the series file.
+func (f *SeriesFile) Reopen() error {
+	if err := f.SeriesFile.Close(); err != nil {
+		return err
+	}
+	f.SeriesFile = tsdb.NewSeriesFile(f.SeriesFile.Path())
+	return f.SeriesFile.Open()
+}
+
+// ForceCompact executes an immediate compaction across all partitions.
+func (f *SeriesFile) ForceCompact() error {
+	for _, p := range f.Partitions() {
+		if err := tsdb.NewSeriesPartitionCompactor().Compact(p); err != nil {
+			return err
+		}
+	}
+	return nil
+}
diff --git a/tsdb/series_index.go b/tsdb/series_index.go
index 1906c39854..1dab0ac095 100644
--- a/tsdb/series_index.go
+++ b/tsdb/series_index.go
@@ -156,8 +156,10 @@ func (idx *SeriesIndex) Delete(id SeriesID) {
 
 // IsDeleted returns true if series id has been deleted.
 func (idx *SeriesIndex) IsDeleted(id SeriesID) bool {
-	_, ok := idx.tombstones[id]
-	return ok
+	if _, ok := idx.tombstones[id]; ok {
+		return true
+	}
+	return idx.FindOffsetByID(id) == 0
 }
 
 func (idx *SeriesIndex) execEntry(flag uint8, id SeriesIDTyped, offset int64, key []byte) {
@@ -263,6 +265,11 @@ func (idx *SeriesIndex) Clone() *SeriesIndex {
 		tombstones[id] = struct{}{}
 	}
 
+	idOffsetMap := make(map[SeriesID]int64)
+	for k, v := range idx.idOffsetMap {
+		idOffsetMap[k] = v
+	}
+
 	return &SeriesIndex{
 		path:         idx.path,
 		count:        idx.count,
@@ -274,6 +281,7 @@ func (idx *SeriesIndex) Clone() *SeriesIndex {
 		keyIDData:    idx.keyIDData,
 		idOffsetData: idx.idOffsetData,
 		tombstones:   tombstones,
+		idOffsetMap:  idOffsetMap,
 	}
 }
 
diff --git a/tsdb/series_partition.go b/tsdb/series_partition.go
index b6c926b688..aafd2e6242 100644
--- a/tsdb/series_partition.go
+++ b/tsdb/series_partition.go
@@ -339,6 +339,13 @@ func (p *SeriesPartition) DeleteSeriesID(id SeriesID) error {
 		return err
 	}
 
+	// Flush active segment write.
+	if segment := p.activeSegment(); segment != nil {
+		if err := segment.Flush(); err != nil {
+			return err
+		}
+	}
+
 	// Mark tombstone in memory.
 	p.index.Delete(id)
 
@@ -580,7 +587,7 @@ func (c *SeriesPartitionCompactor) compactIndexTo(index *SeriesIndex, seriesN ui
 
 		if err := segment.ForEachEntry(func(flag uint8, id SeriesIDTyped, offset int64, key []byte) error {
 			// Make sure we don't go past the offset where the compaction began.
-			if offset >= index.maxOffset {
+			if offset > index.maxOffset {
 				return errDone
 			}
 
@@ -604,14 +611,14 @@ func (c *SeriesPartitionCompactor) compactIndexTo(index *SeriesIndex, seriesN ui
 
 			untypedID := id.SeriesID()
 
+			// Save max series identifier processed.
+			hdr.MaxSeriesID, hdr.MaxOffset = untypedID, offset
+
 			// Ignore entry if tombstoned.
 			if index.IsDeleted(untypedID) {
 				return nil
 			}
 
-			// Save max series identifier processed.
-			hdr.MaxSeriesID, hdr.MaxOffset = untypedID, offset
-
 			// Insert into maps.
 			c.insertIDOffsetMap(idOffsetMap, hdr.Capacity, untypedID, offset)
 			return c.insertKeyIDMap(keyIDMap, hdr.Capacity, segments, key, offset, id)