diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6e078d282e4..2ae087cbc19 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -96,6 +96,7 @@
 * [BUGFIX] Fixed shuffle sharding consistency when zone-awareness is enabled and the shard size is increased or instances in a new zone are added. #3299
 * [BUGFIX] Fixed Gossip memberlist members joining when addresses are configured using DNS-based service discovery. #3360
 * [BUGFIX] Ingester: fail to start an ingester running the blocks storage, if unable to load any existing TSDB at startup. #3354
+* [BUGFIX] Blocks storage: Avoid deletion of blocks in the ingester which are not shipped to the storage yet. #3346
 
 ## 1.4.0 / 2020-10-02
 
diff --git a/pkg/ingester/ingester_v2.go b/pkg/ingester/ingester_v2.go
index 249361a88c0..1851fd79500 100644
--- a/pkg/ingester/ingester_v2.go
+++ b/pkg/ingester/ingester_v2.go
@@ -11,6 +11,7 @@ import (
 	"time"
 
 	"github.com/go-kit/kit/log/level"
+	"github.com/oklog/ulid"
 	"github.com/pkg/errors"
 	"github.com/prometheus/client_golang/prometheus"
 	"github.com/prometheus/client_golang/prometheus/promauto"
@@ -110,6 +111,32 @@ func (u *userTSDB) PostDeletion(metrics ...labels.Labels) {
 	}
 }
 
+// blocksToDelete filters the input blocks and returns the blocks which are safe to be deleted from the ingester.
+func (u *userTSDB) blocksToDelete(blocks []*tsdb.Block) map[ulid.ULID]struct{} {
+	if u.DB == nil {
+		return nil
+	}
+	deletable := tsdb.DefaultBlocksToDelete(u.DB)(blocks)
+	if u.shipper == nil {
+		return deletable
+	}
+
+	shipperMeta, err := shipper.ReadMetaFile(u.Dir())
+	if err != nil {
+		// If there is any issue with the shipper, we should be conservative and not delete anything.
+		level.Error(util.Logger).Log("msg", "failed to read shipper meta during deletion of blocks", "user", u.userID, "err", err)
+		return nil
+	}
+
+	result := map[ulid.ULID]struct{}{}
+	for _, shippedID := range shipperMeta.Uploaded {
+		if _, ok := deletable[shippedID]; ok {
+			result[shippedID] = struct{}{}
+		}
+	}
+	return result
+}
+
 func (u *userTSDB) isIdle(now time.Time, idle time.Duration) bool {
 	lu := u.lastUpdate.Load()
 
@@ -972,6 +999,7 @@ func (i *Ingester) createTSDB(userID string) (*userTSDB, error) {
 		StripeSize:              i.cfg.BlocksStorageConfig.TSDB.StripeSize,
 		WALCompression:          i.cfg.BlocksStorageConfig.TSDB.WALCompressionEnabled,
 		SeriesLifecycleCallback: userDB,
+		BlocksToDelete:          userDB.blocksToDelete,
 	})
 	if err != nil {
 		return nil, errors.Wrapf(err, "failed to open TSDB: %s", udir)
diff --git a/pkg/ingester/ingester_v2_test.go b/pkg/ingester/ingester_v2_test.go
index aa59263a2e0..8e7a9c57089 100644
--- a/pkg/ingester/ingester_v2_test.go
+++ b/pkg/ingester/ingester_v2_test.go
@@ -17,6 +17,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/oklog/ulid"
 	"github.com/pkg/errors"
 	"github.com/prometheus/client_golang/prometheus"
 	"github.com/prometheus/client_golang/prometheus/testutil"
@@ -27,6 +28,7 @@ import (
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/mock"
 	"github.com/stretchr/testify/require"
+	"github.com/thanos-io/thanos/pkg/shipper"
 	"github.com/weaveworks/common/httpgrpc"
 	"github.com/weaveworks/common/middleware"
 	"github.com/weaveworks/common/user"
@@ -2213,3 +2215,87 @@ func TestIngester_CloseTSDBsOnShutdown(t *testing.T) {
 	db = i.getTSDB(userID)
 	require.Nil(t, db)
 }
+
+func TestIngesterNotDeleteUnshippedBlocks(t *testing.T) {
+	chunkRange := 2 * time.Hour
+	chunkRangeMilliSec := chunkRange.Milliseconds()
+	cfg := defaultIngesterTestConfig()
+	cfg.BlocksStorageConfig.TSDB.BlockRanges = []time.Duration{chunkRange}
+	cfg.BlocksStorageConfig.TSDB.Retention = time.Millisecond // Which means delete all but first block.
+	cfg.LifecyclerConfig.JoinAfter = 0
+
+	// Create ingester
+	i, cleanup, err := newIngesterMockWithTSDBStorage(cfg, nil)
+	require.NoError(t, err)
+	t.Cleanup(cleanup)
+
+	require.NoError(t, services.StartAndAwaitRunning(context.Background(), i))
+	t.Cleanup(func() {
+		_ = services.StopAndAwaitTerminated(context.Background(), i)
+	})
+
+	// Wait until it's ACTIVE
+	test.Poll(t, 10*time.Millisecond, ring.ACTIVE, func() interface{} {
+		return i.lifecycler.GetState()
+	})
+
+	// Push some data to create 3 blocks.
+	ctx := user.InjectOrgID(context.Background(), userID)
+	for j := int64(0); j < 5; j++ {
+		req, _, _ := mockWriteRequest(labels.Labels{{Name: labels.MetricName, Value: "test"}}, 0, j*chunkRangeMilliSec)
+		_, err := i.v2Push(ctx, req)
+		require.NoError(t, err)
+	}
+
+	db := i.getTSDB(userID)
+	require.NotNil(t, db)
+	require.Nil(t, db.Compact())
+
+	oldBlocks := db.Blocks()
+	require.Equal(t, 3, len(oldBlocks))
+
+	// Saying that we have shipped the second block, so only that should get deleted.
+	require.Nil(t, shipper.WriteMetaFile(nil, db.Dir(), &shipper.Meta{
+		Version:  shipper.MetaVersion1,
+		Uploaded: []ulid.ULID{oldBlocks[1].Meta().ULID},
+	}))
+
+	// Add more samples that could trigger another compaction and hence reload of blocks.
+	for j := int64(5); j < 6; j++ {
+		req, _, _ := mockWriteRequest(labels.Labels{{Name: labels.MetricName, Value: "test"}}, 0, j*chunkRangeMilliSec)
+		_, err := i.v2Push(ctx, req)
+		require.NoError(t, err)
+	}
+	require.Nil(t, db.Compact())
+
+	// Only the second block should be gone along with a new block.
+	newBlocks := db.Blocks()
+	require.Equal(t, 3, len(newBlocks))
+	require.Equal(t, oldBlocks[0].Meta().ULID, newBlocks[0].Meta().ULID)    // First block remains same.
+	require.Equal(t, oldBlocks[2].Meta().ULID, newBlocks[1].Meta().ULID)    // 3rd block becomes 2nd now.
+	require.NotEqual(t, oldBlocks[1].Meta().ULID, newBlocks[2].Meta().ULID) // The new block won't match previous 2nd block.
+
+	// Shipping 2 more blocks, hence all the blocks from first round.
+	require.Nil(t, shipper.WriteMetaFile(nil, db.Dir(), &shipper.Meta{
+		Version:  shipper.MetaVersion1,
+		Uploaded: []ulid.ULID{oldBlocks[1].Meta().ULID, newBlocks[0].Meta().ULID, newBlocks[1].Meta().ULID},
+	}))
+
+	// Add more samples that could trigger another compaction and hence reload of blocks.
+	for j := int64(6); j < 7; j++ {
+		req, _, _ := mockWriteRequest(labels.Labels{{Name: labels.MetricName, Value: "test"}}, 0, j*chunkRangeMilliSec)
+		_, err := i.v2Push(ctx, req)
+		require.NoError(t, err)
+	}
+	require.Nil(t, db.Compact())
+
+	// All blocks from the old blocks should be gone now.
+	newBlocks2 := db.Blocks()
+	require.Equal(t, 2, len(newBlocks2))
+
+	require.Equal(t, newBlocks[2].Meta().ULID, newBlocks2[0].Meta().ULID) // Block created in last round.
+	for _, b := range oldBlocks {
+		// Second block is not one among old blocks.
+		require.NotEqual(t, b.Meta().ULID, newBlocks2[1].Meta().ULID)
+	}
+}