diff --git a/pkg/storage/stores/shipper/compactor/table.go b/pkg/storage/stores/shipper/compactor/table.go
index 33f2758fb7a0..1d051d9c171a 100644
--- a/pkg/storage/stores/shipper/compactor/table.go
+++ b/pkg/storage/stores/shipper/compactor/table.go
@@ -107,6 +107,11 @@ func (t *table) compact() error {
 						return
 					}
 
+					// The s3 client can also return the directory itself in the ListObjects.
+					if shipper_util.IsDirectory(objectKey) {
+						continue
+					}
+
 					var dbName string
 					dbName, err = shipper_util.GetDBNameFromObjectKey(objectKey)
 					if err != nil {
diff --git a/pkg/storage/stores/shipper/downloads/table.go b/pkg/storage/stores/shipper/downloads/table.go
index 2dc42178a62e..1f1d224f7e9b 100644
--- a/pkg/storage/stores/shipper/downloads/table.go
+++ b/pkg/storage/stores/shipper/downloads/table.go
@@ -209,8 +209,11 @@ func (t *Table) init(ctx context.Context, spanLogger log.Logger) (err error) {
 
 	level.Debug(spanLogger).Log("total-files-downloaded", len(objects))
 
+	objects = shipper_util.RemoveDirectories(objects)
+
 	// open all the downloaded dbs
 	for _, object := range objects {
+
 		dbName, err := getDBNameFromObjectKey(object.Key)
 		if err != nil {
 			return err
@@ -408,6 +411,8 @@ func (t *Table) checkStorageForUpdates(ctx context.Context) (toDownload []chunk.
 	t.dbsMtx.RLock()
 	defer t.dbsMtx.RUnlock()
 
+	objects = shipper_util.RemoveDirectories(objects)
+
 	for _, object := range objects {
 		dbName, err := getDBNameFromObjectKey(object.Key)
 		if err != nil {
@@ -506,6 +511,11 @@ func (t *Table) doParallelDownload(ctx context.Context, objects []chunk.StorageO
 					break
 				}
 
+				// The s3 client can also return the directory itself in the ListObjects.
+				if shipper_util.IsDirectory(object.Key) {
+					continue
+				}
+
 				var dbName string
 				dbName, err = getDBNameFromObjectKey(object.Key)
 				if err != nil {
diff --git a/pkg/storage/stores/shipper/util/util.go b/pkg/storage/stores/shipper/util/util.go
index 8861043948d1..5189e1607121 100644
--- a/pkg/storage/stores/shipper/util/util.go
+++ b/pkg/storage/stores/shipper/util/util.go
@@ -8,6 +8,7 @@ import (
 	"runtime/debug"
 	"strings"
 
+	"github.com/cortexproject/cortex/pkg/chunk"
 	"github.com/cortexproject/cortex/pkg/chunk/local"
 	"go.etcd.io/bbolt"
 
@@ -155,3 +156,20 @@ func safeOpenBoltDbFile(path string, ret chan *result) {
 	res.boltdb = b
 	res.err = err
 }
+
+// RemoveDirectories will return a new slice with any StorageObjects identified as directories removed.
+func RemoveDirectories(incoming []chunk.StorageObject) []chunk.StorageObject {
+	outgoing := make([]chunk.StorageObject, 0, len(incoming))
+	for _, o := range incoming {
+		if IsDirectory(o.Key) {
+			continue
+		}
+		outgoing = append(outgoing, o)
+	}
+	return outgoing
+}
+
+// IsDirectory will return true if the string ends in a forward slash
+func IsDirectory(key string) bool {
+	return strings.HasSuffix(key, "/")
+}
diff --git a/pkg/storage/stores/shipper/util/util_test.go b/pkg/storage/stores/shipper/util/util_test.go
index 4943cad55cce..03d39f07025a 100644
--- a/pkg/storage/stores/shipper/util/util_test.go
+++ b/pkg/storage/stores/shipper/util/util_test.go
@@ -7,7 +7,9 @@ import (
 	"path/filepath"
 	"testing"
 
+	"github.com/cortexproject/cortex/pkg/chunk"
 	"github.com/cortexproject/cortex/pkg/chunk/local"
+	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
 	"github.com/grafana/loki/pkg/storage/stores/shipper/testutil"
@@ -76,3 +78,76 @@ func Test_CompressFile(t *testing.T) {
 
 	require.Equal(t, testData, b)
 }
+
+func TestRemoveDirectories(t *testing.T) {
+	tests := []struct {
+		name     string
+		incoming []chunk.StorageObject
+		expected []chunk.StorageObject
+	}{
+		{
+			name: "no trailing slash",
+			incoming: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj2"},
+				{Key: "obj3"},
+			},
+			expected: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj2"},
+				{Key: "obj3"},
+			},
+		},
+		{
+			name: "one trailing slash",
+			incoming: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj2/"},
+				{Key: "obj3"},
+			},
+			expected: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj3"},
+			},
+		},
+		{
+			name: "only trailing slash",
+			incoming: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj2"},
+				{Key: "/"},
+			},
+			expected: []chunk.StorageObject{
+				{Key: "obj1"},
+				{Key: "obj2"},
+			},
+		},
+		{
+			name: "all trailing slash",
+			incoming: []chunk.StorageObject{
+				{Key: "/"},
+				{Key: "/"},
+				{Key: "/"},
+			},
+			expected: []chunk.StorageObject{},
+		},
+		{
+			name: "internal slash",
+			incoming: []chunk.StorageObject{
+				{Key: "test/test1"},
+				{Key: "te/st"},
+				{Key: "/sted"},
+			},
+			expected: []chunk.StorageObject{
+				{Key: "test/test1"},
+				{Key: "te/st"},
+				{Key: "/sted"},
+			},
+		},
+	}
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			assert.Equal(t, test.expected, RemoveDirectories(test.incoming))
+		})
+	}
+}