diff --git a/CHANGELOG.md b/CHANGELOG.md
index d64e6410890..90a7713d05f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,19 @@ We use *breaking* word for marking changes that are not backward compatible (rel
 
 ### Fixed
 
+- [#2501](https://github.com/thanos-io/thanos/pull/2501) Query: gracefully handle additional fields in `SeriesResponse` protobuf message that may be added in the future.
+
+## [v0.12.1](https://github.com/thanos-io/thanos/releases/tag/v0.12.1) - 2020.04.20
+
+### Fixed
+
+- [#2411](https://github.com/thanos-io/thanos/pull/2411) Query: fix a bug where queries might not time out sometimes due to issues with one or more StoreAPIs.
+- [#2474](https://github.com/thanos-io/thanos/pull/2474) Store: fix a panic caused by concurrent memory access during block filtering.
+- [#2472](https://github.com/thanos-io/thanos/pull/2472) Compact: fix a bug where partial blocks were never deleted, causing spam of warnings.
+- [#2484](https://github.com/thanos-io/thanos/pull/2484) Query/Ruler: fix issue #2483, when web.route-prefix is set, it is added twice in HTTP router prefix.
+
+### Fixed
+
 - [#2416](https://github.com/thanos-io/thanos/pull/2416) Bucket: fixes issue #2416 bug in `inspect --sort-by` doesn't work correctly in all cases
 - [#2411](https://github.com/thanos-io/thanos/pull/2411) Query: fix a bug where queries might not time out sometimes due to issues with one or more StoreAPIs
 
diff --git a/VERSION b/VERSION
index ac454c6a1fc..34a83616bb5 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.12.0
+0.12.1
diff --git a/cmd/thanos/compact.go b/cmd/thanos/compact.go
index 5e297632df7..fb1b2b207d7 100644
--- a/cmd/thanos/compact.go
+++ b/cmd/thanos/compact.go
@@ -420,7 +420,7 @@ func runCompact(
 		}
 
 		// No need to resync before partial uploads and delete marked blocks. Last sync should be valid.
-		compact.BestEffortCleanAbortedPartialUploads(ctx, logger, sy.Partial(), bkt, partialUploadDeleteAttempts, blocksMarkedForDeletion)
+		compact.BestEffortCleanAbortedPartialUploads(ctx, logger, sy.Partial(), bkt, partialUploadDeleteAttempts, blocksCleaned, blockCleanupFailures)
 		if err := blocksCleaner.DeleteMarkedBlocks(ctx); err != nil {
 			return errors.Wrap(err, "error cleaning blocks")
 		}
diff --git a/cmd/thanos/query.go b/cmd/thanos/query.go
index a21565c59a4..2735cd76c20 100644
--- a/cmd/thanos/query.go
+++ b/cmd/thanos/query.go
@@ -8,7 +8,6 @@ import (
 	"fmt"
 	"math"
 	"net/http"
-	"path"
 	"strings"
 	"time"
 
@@ -357,7 +356,7 @@ func runQuery(
 
 		api := v1.NewAPI(logger, reg, engine, queryableCreator, enableAutodownsampling, enablePartialResponse, replicaLabels, instantDefaultMaxSourceResolution)
 
-		api.Register(router.WithPrefix(path.Join(webRoutePrefix, "/api/v1")), tracer, logger, ins)
+		api.Register(router.WithPrefix("/api/v1"), tracer, logger, ins)
 
 		srv := httpserver.New(logger, reg, comp, httpProbe,
 			httpserver.WithListen(httpBindAddr),
diff --git a/cmd/thanos/rule.go b/cmd/thanos/rule.go
index 3c021dec2b6..33889f7c996 100644
--- a/cmd/thanos/rule.go
+++ b/cmd/thanos/rule.go
@@ -8,7 +8,6 @@ import (
 	"math/rand"
 	"net/http"
 	"net/url"
-	"path"
 	"path/filepath"
 	"strconv"
 	"strings"
@@ -576,7 +575,7 @@ func runRule(
 		ui.NewRuleUI(logger, reg, ruleMgr, alertQueryURL.String(), webExternalPrefix, webPrefixHeaderName).Register(router, ins)
 
 		api := v1.NewAPI(logger, reg, ruleMgr)
-		api.Register(router.WithPrefix(path.Join(webRoutePrefix, "/api/v1")), tracer, logger, ins)
+		api.Register(router.WithPrefix("/api/v1"), tracer, logger, ins)
 
 		srv := httpserver.New(logger, reg, comp, httpProbe,
 			httpserver.WithListen(httpBindAddr),
diff --git a/docs/release-process.md b/docs/release-process.md
index c22074d1af1..5beb423c661 100644
--- a/docs/release-process.md
+++ b/docs/release-process.md
@@ -33,7 +33,7 @@ Release shepherd responsibilities:
 | Release   | Time of first RC         | Shepherd (GitHub handle) |
 |-----------|--------------------------|--------------------------|
 | v0.13.0   | (planned) 2020.05.13     | `TBD`                    |
-| v0.12.0   | (planned) 2020.04.01     | `@squat`                 |
+| v0.12.0   | 2020.04.15               | `@squat`                 |
 | v0.11.0   | 2020.02.19               | `@metalmatze`            |
 | v0.10.0   | 2020.01.08               | `@GiedriusS`             |
 | v0.9.0    | 2019.11.26               | `@bwplotka`              |
diff --git a/pkg/block/fetcher.go b/pkg/block/fetcher.go
index 7f21d4d8016..29d67735e2a 100644
--- a/pkg/block/fetcher.go
+++ b/pkg/block/fetcher.go
@@ -550,6 +550,7 @@ var _ MetadataFilter = &DeduplicateFilter{}
 // Not go-routine safe.
 type DeduplicateFilter struct {
 	duplicateIDs []ulid.ULID
+	mu           sync.Mutex
 }
 
 // NewDeduplicateFilter creates DeduplicateFilter.
@@ -603,11 +604,13 @@ func (f *DeduplicateFilter) filterForResolution(root *Node, metaSlice []*metadat
 
 	duplicateULIDs := getNonRootIDs(root)
 	for _, id := range duplicateULIDs {
+		f.mu.Lock()
 		if metas[id] != nil {
 			f.duplicateIDs = append(f.duplicateIDs, id)
 		}
 		synced.WithLabelValues(duplicateMeta).Inc()
 		delete(metas, id)
+		f.mu.Unlock()
 	}
 }
 
diff --git a/pkg/compact/clean.go b/pkg/compact/clean.go
index 53cfb169083..8d99927d515 100644
--- a/pkg/compact/clean.go
+++ b/pkg/compact/clean.go
@@ -27,7 +27,8 @@ func BestEffortCleanAbortedPartialUploads(
 	partial map[ulid.ULID]error,
 	bkt objstore.Bucket,
 	deleteAttempts prometheus.Counter,
-	blocksMarkedForDeletion prometheus.Counter,
+	blockCleanups prometheus.Counter,
+	blockCleanupFailures prometheus.Counter,
 ) {
 	level.Info(logger).Log("msg", "started cleaning of aborted partial uploads")
 
@@ -45,10 +46,15 @@ func BestEffortCleanAbortedPartialUploads(
 
 		deleteAttempts.Inc()
 		level.Info(logger).Log("msg", "found partially uploaded block; marking for deletion", "block", id)
-		if err := block.MarkForDeletion(ctx, logger, bkt, id, blocksMarkedForDeletion); err != nil {
-			level.Warn(logger).Log("msg", "failed to delete aborted partial upload; skipping", "block", id, "thresholdAge", PartialUploadThresholdAge, "err", err)
-			return
+		// We don't gather any information about deletion marks for partial blocks, so let's simply remove it. We waited
+		// long PartialUploadThresholdAge already.
+		// TODO(bwplotka): Fix some edge cases: https://github.com/thanos-io/thanos/issues/2470 .
+		if err := block.Delete(ctx, logger, bkt, id); err != nil {
+			blockCleanupFailures.Inc()
+			level.Warn(logger).Log("msg", "failed to delete aborted partial upload; will retry in next iteration", "block", id, "thresholdAge", PartialUploadThresholdAge, "err", err)
+			continue
 		}
+		blockCleanups.Inc()
 		level.Info(logger).Log("msg", "deleted aborted partial upload", "block", id, "thresholdAge", PartialUploadThresholdAge)
 	}
 	level.Info(logger).Log("msg", "cleaning of aborted partial uploads done")
diff --git a/pkg/compact/clean_test.go b/pkg/compact/clean_test.go
index 1321c888ba6..ea0f840c696 100644
--- a/pkg/compact/clean_test.go
+++ b/pkg/compact/clean_test.go
@@ -59,22 +59,19 @@ func TestBestEffortCleanAbortedPartialUploads(t *testing.T) {
 	testutil.Ok(t, bkt.Upload(ctx, path.Join(shouldIgnoreID2.String(), "chunks", "000001"), &fakeChunk))
 
 	deleteAttempts := promauto.With(nil).NewCounter(prometheus.CounterOpts{})
-	blocksMarkedForDeletion := promauto.With(nil).NewCounter(prometheus.CounterOpts{})
-
+	blockCleanups := promauto.With(nil).NewCounter(prometheus.CounterOpts{})
+	blockCleanupFailures := promauto.With(nil).NewCounter(prometheus.CounterOpts{})
 	_, partial, err := metaFetcher.Fetch(ctx)
 	testutil.Ok(t, err)
 
-	BestEffortCleanAbortedPartialUploads(ctx, logger, partial, bkt, deleteAttempts, blocksMarkedForDeletion)
+	BestEffortCleanAbortedPartialUploads(ctx, logger, partial, bkt, deleteAttempts, blockCleanups, blockCleanupFailures)
 	testutil.Equals(t, 1.0, promtest.ToFloat64(deleteAttempts))
+	testutil.Equals(t, 1.0, promtest.ToFloat64(blockCleanups))
+	testutil.Equals(t, 0.0, promtest.ToFloat64(blockCleanupFailures))
 
 	exists, err := bkt.Exists(ctx, path.Join(shouldDeleteID.String(), "chunks", "000001"))
 	testutil.Ok(t, err)
-	testutil.Equals(t, true, exists)
-
-	exists, err = bkt.Exists(ctx, path.Join(shouldDeleteID.String(), metadata.DeletionMarkFilename))
-	testutil.Ok(t, err)
-	testutil.Equals(t, true, exists)
-	testutil.Equals(t, 1.0, promtest.ToFloat64(blocksMarkedForDeletion))
+	testutil.Equals(t, false, exists)
 
 	exists, err = bkt.Exists(ctx, path.Join(shouldIgnoreID1.String(), "chunks", "000001"))
 	testutil.Ok(t, err)
diff --git a/pkg/query/querier.go b/pkg/query/querier.go
index 898db30fc1b..0299374d3fe 100644
--- a/pkg/query/querier.go
+++ b/pkg/query/querier.go
@@ -124,10 +124,12 @@ func (s *seriesServer) Send(r *storepb.SeriesResponse) error {
 		return nil
 	}
 
-	if r.GetSeries() == nil {
-		return errors.New("no seriesSet")
+	if r.GetSeries() != nil {
+		s.seriesSet = append(s.seriesSet, *r.GetSeries())
+		return nil
 	}
-	s.seriesSet = append(s.seriesSet, *r.GetSeries())
+
+	// Unsupported field, skip.
 	return nil
 }
 
diff --git a/pkg/store/proxy.go b/pkg/store/proxy.go
index c071848c051..36da2e62fdd 100644
--- a/pkg/store/proxy.go
+++ b/pkg/store/proxy.go
@@ -432,13 +432,15 @@ func startStreamSeriesSet(
 
 			if w := rr.r.GetWarning(); w != "" {
 				s.warnCh.send(storepb.NewWarnSeriesResponse(errors.New(w)))
-				continue
 			}
-			select {
-			case s.recvCh <- rr.r.GetSeries():
-			case <-ctx.Done():
-				s.handleErr(errors.Wrapf(ctx.Err(), "failed to receive any data from %s", s.name), done)
-				return
+
+			if series := rr.r.GetSeries(); series != nil {
+				select {
+				case s.recvCh <- series:
+				case <-ctx.Done():
+					s.handleErr(errors.Wrapf(ctx.Err(), "failed to receive any data from %s", s.name), done)
+					return
+				}
 			}
 		}
 	}()
diff --git a/pkg/store/proxy_test.go b/pkg/store/proxy_test.go
index 8e8b6022d4e..32416d8b292 100644
--- a/pkg/store/proxy_test.go
+++ b/pkg/store/proxy_test.go
@@ -1379,10 +1379,12 @@ func (s *storeSeriesServer) Send(r *storepb.SeriesResponse) error {
 		return nil
 	}
 
-	if r.GetSeries() == nil {
-		return errors.New("no seriesSet")
+	if r.GetSeries() != nil {
+		s.SeriesSet = append(s.SeriesSet, *r.GetSeries())
+		return nil
 	}
-	s.SeriesSet = append(s.SeriesSet, *r.GetSeries())
+
+	// Unsupported field, skip.
 	return nil
 }
 
diff --git a/test/e2e/compact_test.go b/test/e2e/compact_test.go
index 5e4b601dcff..9f4dd0d65fb 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 +19,13 @@ 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/client_golang/prometheus/promauto"
 	"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 +35,26 @@ 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) {
+	if delay == 0*time.Second {
+		return e2eutil.CreateBlock(ctx, dir, b.series, 120, b.mint, b.maxt, b.extLset, 0)
+	}
+	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 +280,7 @@ 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 +294,73 @@ 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, promauto.With(nil).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, promauto.With(nil).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(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, promauto.With(nil).NewCounter(prometheus.CounterOpts{})))
+		testutil.Ok(t, objstore.UploadDir(ctx, logger, bkt, path.Join(dir, id.String()), id.String()))
+	}
 
 	svcConfig := client.BucketConfig{
 		Type: client.S3,
@@ -299,7 +375,7 @@ func TestCompactWithStoreGateway(t *testing.T) {
 	str, err := e2ethanos.NewStoreGW(s.SharedDir(), "1", svcConfig)
 	testutil.Ok(t, err)
 	testutil.Ok(t, s.StartAndWaitReady(str))
-	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs))), "thanos_blocks_meta_synced"))
+	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7)), "thanos_blocks_meta_synced"))
 	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
 	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_modified"))
 
@@ -349,12 +425,50 @@ func TestCompactWithStoreGateway(t *testing.T) {
 			{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
 		},
 	)
+	// Store view:
+	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7)), "thanos_blocks_meta_synced"))
+	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
+	testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_modified"))
+
+	expectedEndVector := model.Vector{
+		// NOTE(bwplotka): Even after deduplication some series has still replica labels. This is because those blocks did not overlap yet with anything.
+		// This is fine as querier deduplication will remove it if needed.
+		{Value: 360, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "no-compaction", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "compaction-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "compaction-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "compaction-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "compaction-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "6", "case": "compaction-ready", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "compaction-ready-after-dedup"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "compaction-ready-after-dedup"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "compaction-ready-after-dedup"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "compaction-ready-after-dedup"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "6", "case": "compaction-ready-after-dedup", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "a-partial-overlap-dedup-ready"}},
+		{Value: 360, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "a-partial-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "a-partial-overlap-dedup-ready", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "a-partial-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "a-partial-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "a-partial-overlap-dedup-ready", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "partial-multi-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "partial-multi-replica-overlap-dedup-ready", "replica": "1", "rule_replica": "1"}},
+		{Value: 240, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "partial-multi-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "partial-multi-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "partial-multi-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "partial-multi-replica-overlap-dedup-ready", "replica": "1", "rule_replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "full-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "full-replica-overlap-dedup-ready"}},
+		{Value: 240, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "full-replica-overlap-dedup-ready"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
+		{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
+	}
 
 	t.Run("no replica label with overlaps should halt compactor", func(t *testing.T) {
 		c, err := e2ethanos.NewCompactor(s.SharedDir(), "expect-to-halt", svcConfig, nil)
 		testutil.Ok(t, err)
 		testutil.Ok(t, s.StartAndWaitReady(c))
-		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs))), "thanos_blocks_meta_synced"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7)), "thanos_blocks_meta_synced"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_modified"))
 
@@ -364,7 +478,9 @@ func TestCompactWithStoreGateway(t *testing.T) {
 		// We expect no ops.
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_iterations_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_blocks_cleaned_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_block_cleanup_failures_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_blocks_marked_for_deletion_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_aborted_partial_uploads_deletion_attempts_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_compactions_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_vertical_compactions_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(1), "thanos_compact_group_compactions_failures_total"))
@@ -380,7 +496,8 @@ func TestCompactWithStoreGateway(t *testing.T) {
 
 		testutil.Ok(t, s.Stop(c))
 	})
-	t.Run("native vertical deduplication should kick in", func(t *testing.T) {
+	t.Run("dedup enabled; compactor should work as expected", func(t *testing.T) {
+		// We expect 2x 4-block compaction, 2-block vertical compaction, 2x 3-block compaction.
 		c, err := e2ethanos.NewCompactor(s.SharedDir(), "working", svcConfig, nil, "--deduplication.replica-label=replica", "--deduplication.replica-label=rule_replica")
 		testutil.Ok(t, err)
 		testutil.Ok(t, s.StartAndWaitReady(c))
@@ -388,10 +505,10 @@ func TestCompactWithStoreGateway(t *testing.T) {
 		// NOTE: We cannot assert on intermediate `thanos_blocks_meta_` metrics as those are gauge and change dynamically due to many
 		// compaction groups. Wait for at least first compaction iteration (next is in 5m).
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Greater(0), "thanos_compactor_iterations_total"))
-
-		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(16), "thanos_compactor_blocks_cleaned_total"))
-		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(16), "thanos_compactor_blocks_marked_for_deletion_total"))
-
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(2), "thanos_compactor_blocks_cleaned_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_block_cleanup_failures_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(2*4+2+2*3), "thanos_compactor_blocks_marked_for_deletion_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(2), "thanos_compactor_aborted_partial_uploads_deletion_attempts_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(5), "thanos_compact_group_compactions_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(3), "thanos_compact_group_vertical_compactions_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_compactions_failures_total"))
@@ -401,8 +518,11 @@ func TestCompactWithStoreGateway(t *testing.T) {
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_downsample_total"))
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_downsample_failures_total"))
 
-		// We had 8 deletions based on 3 compactios, so 3 new blocks.
-		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)-16+5)), "thanos_blocks_meta_synced"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(
+			len(rawBlockIDs)+7+
+				5+ // 5 compactions, 5 newly added blocks.
+				-2, // Partial block removed.
+		)), "thanos_blocks_meta_synced"))
 		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
 
 		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_halted"))
@@ -418,43 +538,56 @@ func TestCompactWithStoreGateway(t *testing.T) {
 			promclient.QueryOptions{
 				Deduplicate: false, // This should be false, so that we can be sure deduplication was offline.
 			},
-			model.Vector{
-				// NOTE(bwplotka): Even after deduplication some series has still replica labels. This is because those blocks did not overlap yet with anything.
-				// This is fine as querier deduplication will remove it if needed.
-				{Value: 360, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "no-compaction", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "compaction-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "compaction-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "compaction-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "compaction-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "6", "case": "compaction-ready", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "compaction-ready-after-dedup"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "compaction-ready-after-dedup"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "compaction-ready-after-dedup"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "compaction-ready-after-dedup"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "6", "case": "compaction-ready-after-dedup", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "a-partial-overlap-dedup-ready"}},
-				{Value: 360, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "a-partial-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "a-partial-overlap-dedup-ready", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "a-partial-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "a-partial-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "a-partial-overlap-dedup-ready", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "partial-multi-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "partial-multi-replica-overlap-dedup-ready", "replica": "1", "rule_replica": "1"}},
-				{Value: 240, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "partial-multi-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "partial-multi-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "partial-multi-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "partial-multi-replica-overlap-dedup-ready", "replica": "1", "rule_replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "1", "case": "full-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "full-replica-overlap-dedup-ready"}},
-				{Value: 240, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "2", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "3", "case": "full-replica-overlap-dedup-ready"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "4", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
-				{Value: 120, Metric: map[model.LabelName]model.LabelValue{"a": "1", "b": "5", "case": "full-replica-overlap-dedup-ready", "replica": "1"}},
+			expectedEndVector,
+		)
+		// Store view:
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7+5-2)), "thanos_blocks_meta_synced"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_modified"))
+	})
+
+	t.Run("dedup enabled; no delete delay; compactor should work and remove things as expected", func(t *testing.T) {
+		c, err := e2ethanos.NewCompactor(s.SharedDir(), "working", svcConfig, nil, "--deduplication.replica-label=replica", "--deduplication.replica-label=rule_replica", "--delete-delay=0s")
+		testutil.Ok(t, err)
+		testutil.Ok(t, s.StartAndWaitReady(c))
+
+		// NOTE: We cannot assert on intermediate `thanos_blocks_meta_` metrics as those are gauge and change dynamically due to many
+		// compaction groups. Wait for at least first compaction iteration (next is in 5m).
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Greater(0), "thanos_compactor_iterations_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(16), "thanos_compactor_blocks_cleaned_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_block_cleanup_failures_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_blocks_marked_for_deletion_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_aborted_partial_uploads_deletion_attempts_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_compactions_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_vertical_compactions_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_group_compactions_failures_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(6), "thanos_compact_group_compaction_runs_started_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(6), "thanos_compact_group_compaction_runs_completed_total"))
+
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_downsample_total"))
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compact_downsample_failures_total"))
+
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7+5-16-2)), "thanos_blocks_meta_synced"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
+
+		testutil.Ok(t, c.WaitSumMetrics(e2e.Equals(0), "thanos_compactor_halted"))
+		// Make sure compactor does not modify anything else over time.
+		testutil.Ok(t, s.Stop(c))
+
+		ctx, cancel = context.WithTimeout(context.Background(), 3*time.Minute)
+		defer cancel()
+
+		// Check if query detects new blocks.
+		queryAndAssert(t, ctx, q.HTTPEndpoint(),
+			fmt.Sprintf(`count_over_time({a="1"}[13h] offset %ds)`, int64(time.Since(now.Add(12*time.Hour)).Seconds())),
+			promclient.QueryOptions{
+				Deduplicate: false, // This should be false, so that we can be sure deduplication was offline.
 			},
+			expectedEndVector,
 		)
 
 		// Store view:
-		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)-16+5)), "thanos_blocks_meta_synced"))
+		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(float64(len(rawBlockIDs)+7-16+5-2)), "thanos_blocks_meta_synced"))
 		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_sync_failures_total"))
 		testutil.Ok(t, str.WaitSumMetrics(e2e.Equals(0), "thanos_blocks_meta_modified"))
 	})
diff --git a/test/e2e/e2ethanos/services.go b/test/e2e/e2ethanos/services.go
index c014a36d7b8..c0d4bc7f354 100644
--- a/test/e2e/e2ethanos/services.go
+++ b/test/e2e/e2ethanos/services.go
@@ -373,7 +373,6 @@ func NewCompactor(sharedDir string, name string, bucketConfig client.BucketConfi
 			"--data-dir":                container,
 			"--objstore.config":         string(bktConfigBytes),
 			"--http-address":            ":80",
-			"--delete-delay":            "0s",
 			"--block-sync-concurrency":  "20",
 			"--selector.relabel-config": string(relabelConfigBytes),
 			"--wait":                    "",
diff --git a/tutorials/katacoda/thanos/1-globalview/courseBase.sh b/tutorials/katacoda/thanos/1-globalview/courseBase.sh
index 53b64d03ff0..c06dec0cf94 100644
--- a/tutorials/katacoda/thanos/1-globalview/courseBase.sh
+++ b/tutorials/katacoda/thanos/1-globalview/courseBase.sh
@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 docker pull quay.io/prometheus/prometheus:v2.16.0
-docker pull quay.io/thanos/thanos:v0.12.0
+docker pull quay.io/thanos/thanos:v0.12.1
diff --git a/tutorials/katacoda/thanos/1-globalview/step2.md b/tutorials/katacoda/thanos/1-globalview/step2.md
index ed8bcc1576f..af4b9d15b67 100644
--- a/tutorials/katacoda/thanos/1-globalview/step2.md
+++ b/tutorials/katacoda/thanos/1-globalview/step2.md
@@ -10,7 +10,7 @@ component and can be invoked in a single command.
 Let's take a look at all the Thanos commands:
 
 ```
-docker run --rm quay.io/thanos/thanos:v0.12.0 --help
+docker run --rm quay.io/thanos/thanos:v0.12.1 --help
 ```{{execute}}
 
 You should see multiple commands that solves different purposes.
@@ -53,7 +53,7 @@ docker run -d --net=host --rm \
     -v $(pwd)/prometheus0_eu1.yml:/etc/prometheus/prometheus.yml \
     --name prometheus-0-sidecar-eu1 \
     -u root \
-    quay.io/thanos/thanos:v0.12.0 \
+    quay.io/thanos/thanos:v0.12.1 \
     sidecar \
     --http-address 0.0.0.0:19090 \
     --grpc-address 0.0.0.0:19190 \
@@ -68,7 +68,7 @@ docker run -d --net=host --rm \
     -v $(pwd)/prometheus0_us1.yml:/etc/prometheus/prometheus.yml \
     --name prometheus-0-sidecar-us1 \
     -u root \
-    quay.io/thanos/thanos:v0.12.0 \
+    quay.io/thanos/thanos:v0.12.1 \
     sidecar \
     --http-address 0.0.0.0:19091 \
     --grpc-address 0.0.0.0:19191 \
@@ -81,7 +81,7 @@ docker run -d --net=host --rm \
     -v $(pwd)/prometheus1_us1.yml:/etc/prometheus/prometheus.yml \
     --name prometheus-1-sidecar-us1 \
     -u root \
-    quay.io/thanos/thanos:v0.12.0 \
+    quay.io/thanos/thanos:v0.12.1 \
     sidecar \
     --http-address 0.0.0.0:19092 \
     --grpc-address 0.0.0.0:19192 \
diff --git a/tutorials/katacoda/thanos/1-globalview/step3.md b/tutorials/katacoda/thanos/1-globalview/step3.md
index c7635b46071..8d4b17e84df 100644
--- a/tutorials/katacoda/thanos/1-globalview/step3.md
+++ b/tutorials/katacoda/thanos/1-globalview/step3.md
@@ -28,7 +28,7 @@ Click below snippet to start the Querier.
 ```
 docker run -d --net=host --rm \
     --name querier \
-    quay.io/thanos/thanos:v0.12.0 \
+    quay.io/thanos/thanos:v0.12.1 \
     query \
     --http-address 0.0.0.0:29090 \
     --query.replica-label replica \