diff --git a/CHANGELOG.md b/CHANGELOG.md
index d438abf95d..5e0a971dab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,7 +28,7 @@ We use _breaking :warning:_ to mark changes that are not backward compatible (re
 - [#2732](https://github.com/thanos-io/thanos/pull/2732) Swift: Switched to a new library [ncw/swift](https://github.com/ncw/swift) providing large objects support.
    By default, segments will be uploaded to the same container directory `segments/` if the file is bigger than `1GB`.
    To change the defaults see [the docs](./docs/storage.md#openstack-swift).
-
+- [#3626](https://github.com/thanos-io/thanos/pull/3626) Failed upload of `meta.json` file doesn't cause block cleanup anymore. This has a potential to generate corrupted blocks under specific conditions. Partial block is left in bucket for later cleanup.
 
 
 ## [v0.17.2](https://github.com/thanos-io/thanos/releases/tag/v0.17.2) - 2020.12.07
diff --git a/pkg/block/block.go b/pkg/block/block.go
index 33993bd446..f95e176f51 100644
--- a/pkg/block/block.go
+++ b/pkg/block/block.go
@@ -117,7 +117,11 @@ func Upload(ctx context.Context, logger log.Logger, bkt objstore.Bucket, bdir st
 
 	// Meta.json always need to be uploaded as a last item. This will allow to assume block directories without meta file to be pending uploads.
 	if err := bkt.Upload(ctx, path.Join(id.String(), MetaFilename), &metaEncoded); err != nil {
-		return cleanUp(logger, bkt, id, errors.Wrap(err, "upload meta file"))
+		// Don't call cleanUp here. Despite getting error, meta.json may have been uploaded in certain cases,
+		// and even though cleanUp will not see it yet, meta.json may appear in the bucket later.
+		// (Eg. S3 is known to behave this way when it returns 503 "SlowDown" error).
+		// If meta.json is not uploaded, this will produce partial blocks, but such blocks will be cleaned later.
+		return errors.Wrap(err, "upload meta file")
 	}
 
 	return nil
diff --git a/pkg/block/block_test.go b/pkg/block/block_test.go
index ee473f0b09..076099e9cb 100644
--- a/pkg/block/block_test.go
+++ b/pkg/block/block_test.go
@@ -8,6 +8,7 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"io"
 	"io/ioutil"
 	"os"
 	"path"
@@ -17,6 +18,7 @@ import (
 
 	"github.com/go-kit/kit/log"
 	"github.com/oklog/ulid"
+	"github.com/pkg/errors"
 	"github.com/prometheus/client_golang/prometheus"
 	"github.com/prometheus/client_golang/prometheus/promauto"
 	promtest "github.com/prometheus/client_golang/prometheus/testutil"
@@ -367,3 +369,68 @@ func TestMarkForNoCompact(t *testing.T) {
 		})
 	}
 }
+
+func TestUploadCleanup(t *testing.T) {
+	defer testutil.TolerantVerifyLeak(t)
+
+	ctx := context.Background()
+
+	tmpDir, err := ioutil.TempDir("", "test-block-upload")
+	testutil.Ok(t, err)
+	defer func() { testutil.Ok(t, os.RemoveAll(tmpDir)) }()
+
+	bkt := objstore.NewInMemBucket()
+	b1, err := e2eutil.CreateBlock(ctx, tmpDir, []labels.Labels{
+		{{Name: "a", Value: "1"}},
+		{{Name: "a", Value: "2"}},
+		{{Name: "a", Value: "3"}},
+		{{Name: "a", Value: "4"}},
+		{{Name: "b", Value: "1"}},
+	}, 100, 0, 1000, labels.Labels{{Name: "ext1", Value: "val1"}}, 124)
+	testutil.Ok(t, err)
+
+	{
+		errBkt := errBucket{Bucket: bkt, failSuffix: "/index"}
+
+		uploadErr := Upload(ctx, log.NewNopLogger(), errBkt, path.Join(tmpDir, b1.String()))
+		testutil.Assert(t, errors.Is(uploadErr, errUploadFailed))
+
+		// If upload of index fails, block is deleted.
+		testutil.Equals(t, 1, len(bkt.Objects())) // Only debug meta file is present.
+		testutil.Assert(t, len(bkt.Objects()[path.Join(DebugMetas, fmt.Sprintf("%s.json", b1.String()))]) > 0)
+	}
+
+	{
+		errBkt := errBucket{Bucket: bkt, failSuffix: "/meta.json"}
+
+		uploadErr := Upload(ctx, log.NewNopLogger(), errBkt, path.Join(tmpDir, b1.String()))
+		testutil.Assert(t, errors.Is(uploadErr, errUploadFailed))
+
+		// If upload of meta.json fails, nothing is cleaned up.
+		testutil.Equals(t, 4, len(bkt.Objects()))
+		testutil.Assert(t, len(bkt.Objects()[path.Join(b1.String(), ChunksDirname, "000001")]) > 0)
+		testutil.Assert(t, len(bkt.Objects()[path.Join(b1.String(), IndexFilename)]) > 0)
+		testutil.Assert(t, len(bkt.Objects()[path.Join(b1.String(), MetaFilename)]) > 0)
+		testutil.Assert(t, len(bkt.Objects()[path.Join(DebugMetas, fmt.Sprintf("%s.json", b1.String()))]) > 0)
+	}
+}
+
+var errUploadFailed = errors.New("upload failed")
+
+type errBucket struct {
+	objstore.Bucket
+
+	failSuffix string
+}
+
+func (eb errBucket) Upload(ctx context.Context, name string, r io.Reader) error {
+	err := eb.Bucket.Upload(ctx, name, r)
+	if err != nil {
+		return err
+	}
+
+	if strings.HasSuffix(name, eb.failSuffix) {
+		return errUploadFailed
+	}
+	return nil
+}