diff --git a/test/e2e/compact_test.go b/test/e2e/compact_test.go
index 5e4b601dcff..e3e127a88d4 100644
--- a/test/e2e/compact_test.go
+++ b/test/e2e/compact_test.go
@@ -4,7 +4,9 @@
 package e2e_test
 
 import (
+	"bytes"
 	"context"
+	"encoding/json"
 	"fmt"
 	"net/http"
 	"os"
@@ -17,9 +19,12 @@ import (
 	e2edb "github.com/cortexproject/cortex/integration/e2e/db"
 	"github.com/go-kit/kit/log"
 	"github.com/oklog/ulid"
+	"github.com/prometheus/client_golang/prometheus"
 	"github.com/prometheus/common/model"
 	"github.com/prometheus/prometheus/pkg/labels"
 	"github.com/prometheus/prometheus/pkg/timestamp"
+	"github.com/thanos-io/thanos/pkg/block"
+	"github.com/thanos-io/thanos/pkg/block/metadata"
 	"github.com/thanos-io/thanos/pkg/objstore"
 	"github.com/thanos-io/thanos/pkg/objstore/client"
 	"github.com/thanos-io/thanos/pkg/objstore/s3"
@@ -29,18 +34,23 @@ import (
 	"github.com/thanos-io/thanos/test/e2e/e2ethanos"
 )
 
+type blockDesc struct {
+	series  []labels.Labels
+	extLset labels.Labels
+	mint    int64
+	maxt    int64
+}
+
+func (b *blockDesc) Create(ctx context.Context, dir string, delay time.Duration) (ulid.ULID, error) {
+	return e2eutil.CreateBlockWithBlockDelay(ctx, dir, b.series, 120, b.mint, b.maxt, delay, b.extLset, 0)
+}
+
 func TestCompactWithStoreGateway(t *testing.T) {
 	t.Parallel()
 
-	l := log.NewLogfmtLogger(os.Stdout)
-	type blockDesc struct {
-		series  []labels.Labels
-		extLset labels.Labels
-		mint    int64
-		maxt    int64
-	}
+	logger := log.NewLogfmtLogger(os.Stdout)
 
-	delay := 30 * time.Minute
+	justAfterConsistencyDelay := 30 * time.Minute
 	// Make sure to take realistic timestamp for start. This is to align blocks as if they would be aligned on Prometheus.
 	// To have deterministic compaction, let's have fixed date:
 	now, err := time.Parse(time.RFC3339, "2020-03-24T08:00:00Z")
@@ -266,7 +276,7 @@ func TestCompactWithStoreGateway(t *testing.T) {
 	m := e2edb.NewMinio(8080, bucket)
 	testutil.Ok(t, s.StartAndWaitReady(m))
 
-	bkt, err := s3.NewBucketWithConfig(l, s3.Config{
+	bkt, err := s3.NewBucketWithConfig(logger, s3.Config{
 		Bucket:    bucket,
 		AccessKey: e2edb.MinioAccessKey,
 		SecretKey: e2edb.MinioSecretKey,
@@ -280,11 +290,73 @@ func TestCompactWithStoreGateway(t *testing.T) {
 
 	rawBlockIDs := map[ulid.ULID]struct{}{}
 	for _, b := range blocks {
-		id, err := e2eutil.CreateBlockWithBlockDelay(ctx, dir, b.series, 120, b.mint, b.maxt, delay, b.extLset, 0)
+		id, err := b.Create(ctx, dir, justAfterConsistencyDelay)
 		testutil.Ok(t, err)
-		testutil.Ok(t, objstore.UploadDir(ctx, l, bkt, path.Join(dir, id.String()), id.String()))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
 		rawBlockIDs[id] = struct{}{}
 	}
+	{
+		// On top of that, add couple of other tricky cases with different meta.
+		malformedBase := blockDesc{
+			series:  []labels.Labels{labels.FromStrings("a", "1", "b", "2")},
+			extLset: labels.FromStrings("case", "malformed-things", "replica", "101"),
+			mint:    timestamp.FromTime(now),
+			maxt:    timestamp.FromTime(now.Add(2 * time.Hour)),
+		}
+
+		// New Partial block.
+		id, err := malformedBase.Create(ctx, dir, 0*time.Second)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// New Partial block + deletion mark.
+		id, err = malformedBase.Create(ctx, dir, 0*time.Second)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, block.MarkForDeletion(ctx, logger, bkt, id, prometheus.NewCounter(prometheus.CounterOpts{})))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// Partial block after consistency delay.
+		id, err = malformedBase.Create(ctx, dir, justAfterConsistencyDelay)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// Partial block after consistency delay + deletion mark.
+		id, err = malformedBase.Create(ctx, dir, justAfterConsistencyDelay)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, block.MarkForDeletion(ctx, logger, bkt, id, prometheus.NewCounter(prometheus.CounterOpts{})))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// Partial block after consistency delay + old deletion mark ready to be deleted.
+		id, err = malformedBase.Create(ctx, dir, justAfterConsistencyDelay)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		deletionMark, err := json.Marshal(metadata.DeletionMark{
+			ID: id,
+			// Deletion threshold is usually 2 days.
+			DeletionTime: time.Now().Add(-50 * time.Hour).Unix(),
+			Version:      metadata.DeletionMarkVersion1,
+		})
+		testutil.Ok(t, err)
+		testutil.Ok(t, bkt.Upload(ctx, path.Join(dir, id.String(), metadata.DeletionMarkFilename), bytes.NewBuffer(deletionMark)))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// Partial block after delete threshold.
+		id, err = malformedBase.Create(ctx, dir, 50*time.Hour)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+
+		// Partial block after delete threshold + deletion mark.
+		id, err = malformedBase.Create(ctx, dir, 50*time.Hour)
+		testutil.Ok(t, err)
+		testutil.Ok(t, os.Remove(path.Join(dir, id.String(), metadata.MetaFilename)))
+		testutil.Ok(t, block.MarkForDeletion(ctx, logger, bkt, id, prometheus.NewCounter(prometheus.CounterOpts{})))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+	}
 
 	svcConfig := client.BucketConfig{
 		Type: client.S3,