diff --git a/tsdb/compact.go b/tsdb/compact.go
index 7db7f5284..d5952bec2 100644
--- a/tsdb/compact.go
+++ b/tsdb/compact.go
@@ -471,26 +471,12 @@ func (c *LeveledCompactor) compact(dest string, dirs []string, open []*Block, sh
 	err = c.write(dest, outBlocks, blocks...)
 	if err == nil {
 		ulids := make([]ulid.ULID, len(outBlocks))
+		allOutputBlocksAreEmpty := true
 
 		for ix := range outBlocks {
 			meta := outBlocks[ix].meta
 
-			ulids[ix] = outBlocks[ix].meta.ULID
-
 			if meta.Stats.NumSamples == 0 {
-				for _, b := range bs {
-					b.meta.Compaction.Deletable = true
-					n, err := writeMetaFile(c.logger, b.dir, &b.meta)
-					if err != nil {
-						level.Error(c.logger).Log(
-							"msg", "Failed to write 'Deletable' to meta file after compaction",
-							"ulid", b.meta.ULID,
-							"shard", fmt.Sprintf("%d_of_%d", ix, shardCount),
-						)
-					}
-					b.numBytesMeta = n
-				}
-				ulids[ix] = ulid.ULID{}
 				level.Info(c.logger).Log(
 					"msg", "compact blocks resulted in empty block",
 					"count", len(blocks),
@@ -499,6 +485,9 @@ func (c *LeveledCompactor) compact(dest string, dirs []string, open []*Block, sh
 					"shard", fmt.Sprintf("%d_of_%d", ix, shardCount),
 				)
 			} else {
+				allOutputBlocksAreEmpty = false
+				ulids[ix] = outBlocks[ix].meta.ULID
+
 				level.Info(c.logger).Log(
 					"msg", "compact blocks",
 					"count", len(blocks),
@@ -511,6 +500,22 @@ func (c *LeveledCompactor) compact(dest string, dirs []string, open []*Block, sh
 				)
 			}
 		}
+
+		if allOutputBlocksAreEmpty {
+			// Mark source blocks as deletable.
+			for _, b := range bs {
+				b.meta.Compaction.Deletable = true
+				n, err := writeMetaFile(c.logger, b.dir, &b.meta)
+				if err != nil {
+					level.Error(c.logger).Log(
+						"msg", "Failed to write 'Deletable' to meta file after compaction",
+						"ulid", b.meta.ULID,
+					)
+				}
+				b.numBytesMeta = n
+			}
+		}
+
 		return ulids, nil
 	}
 
diff --git a/tsdb/compact_test.go b/tsdb/compact_test.go
index 87270ffa1..11171a69e 100644
--- a/tsdb/compact_test.go
+++ b/tsdb/compact_test.go
@@ -15,6 +15,7 @@ package tsdb
 
 import (
 	"context"
+	"crypto/rand"
 	"fmt"
 	"io/ioutil"
 	"math"
@@ -574,11 +575,75 @@ func TestCompaction_CompactWithSplitting(t *testing.T) {
 				}
 
 				require.Equal(t, uint64(series), totalSeries)
+
+				// Source blocks are *not* deletable.
+				for _, b := range openBlocks {
+					require.False(t, b.meta.Compaction.Deletable)
+				}
 			})
 		}
 	}
 }
 
+func TestCompaction_CompactEmptyBlocks(t *testing.T) {
+	dir, err := ioutil.TempDir("", "compact")
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, os.RemoveAll(dir))
+	}()
+
+	ranges := [][2]int64{{0, 5000}, {3000, 8000}, {6000, 11000}, {9000, 14000}}
+
+	// Generate blocks.
+	var blockDirs []string
+
+	for _, r := range ranges {
+		// Generate blocks using index and chunk writer. CreateBlock would not return valid block for 0 series.
+		id := ulid.MustNew(ulid.Now(), rand.Reader)
+		m := &BlockMeta{
+			ULID:       id,
+			MinTime:    r[0],
+			MaxTime:    r[1],
+			Compaction: BlockMetaCompaction{Level: 1, Sources: []ulid.ULID{id}},
+			Version:    metaVersion1,
+		}
+
+		bdir := filepath.Join(dir, id.String())
+		require.NoError(t, os.Mkdir(bdir, 0777))
+		require.NoError(t, os.Mkdir(chunkDir(bdir), 0777))
+
+		_, err := writeMetaFile(log.NewNopLogger(), bdir, m)
+		require.NoError(t, err)
+
+		iw, err := index.NewWriter(context.Background(), filepath.Join(bdir, indexFilename))
+		require.NoError(t, err)
+
+		require.NoError(t, iw.AddSymbol("hello"))
+		require.NoError(t, iw.AddSymbol("world"))
+		require.NoError(t, iw.Close())
+
+		blockDirs = append(blockDirs, bdir)
+	}
+
+	c, err := NewLeveledCompactor(context.Background(), nil, log.NewNopLogger(), []int64{0}, nil, nil)
+	require.NoError(t, err)
+
+	blockIDs, err := c.CompactWithSplitting(dir, blockDirs, nil, 5)
+	require.NoError(t, err)
+
+	// There are no output blocks.
+	for _, b := range blockIDs {
+		require.Equal(t, ulid.ULID{}, b)
+	}
+
+	// All source blocks are now marked for deletion.
+	for _, b := range blockDirs {
+		meta, _, err := readMetaFile(b)
+		require.NoError(t, err)
+		require.True(t, meta.Compaction.Deletable)
+	}
+}
+
 func TestCompaction_populateBlock(t *testing.T) {
 	for _, tc := range []struct {
 		title              string