diff --git a/accounts/pkg/indexer/index/cs3/autoincrement.go b/accounts/pkg/indexer/index/cs3/autoincrement.go
index 465521588..ded4d9aa1 100644
--- a/accounts/pkg/indexer/index/cs3/autoincrement.go
+++ b/accounts/pkg/indexer/index/cs3/autoincrement.go
@@ -15,6 +15,7 @@ import (
 	idxerrs "github.com/owncloud/ocis/accounts/pkg/indexer/errors"
 
 	user "github.com/cs3org/go-cs3apis/cs3/identity/user/v1beta1"
+	rpc "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
 	v1beta11 "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
 	provider "github.com/cs3org/go-cs3apis/cs3/storage/provider/v1beta1"
 	"github.com/cs3org/reva/pkg/rgrpc/todo/pool"
@@ -385,3 +386,34 @@ func (idx *Autoincrement) next() (int, error) {
 	}
 	return latest + 1, nil
 }
+
+func (idx *Autoincrement) getAuthenticatedContext(ctx context.Context) (context.Context, error) {
+	t, err := idx.authenticate(ctx)
+	if err != nil {
+		return nil, err
+	}
+	ctx = metadata.AppendToOutgoingContext(ctx, token.TokenHeader, t)
+	return ctx, nil
+}
+
+// Delete deletes the index folder from its storage.
+func (idx *Autoincrement) Delete() error {
+	ctx, err := idx.getAuthenticatedContext(context.Background())
+	if err != nil {
+		return err
+	}
+
+	res, err := idx.storageProvider.Delete(ctx, &provider.DeleteRequest{
+		Ref: &provider.Reference{
+			Spec: &provider.Reference_Path{Path: path.Join("/meta", idx.indexRootDir)},
+		},
+	})
+	if err != nil {
+		return err
+	}
+	if res.Status.Code != rpc.Code_CODE_OK {
+		return fmt.Errorf("error deleting index root dir: %v", idx.indexRootDir)
+	}
+
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/cs3/non_unique.go b/accounts/pkg/indexer/index/cs3/non_unique.go
index c017d791b..d0a9dd923 100644
--- a/accounts/pkg/indexer/index/cs3/non_unique.go
+++ b/accounts/pkg/indexer/index/cs3/non_unique.go
@@ -10,6 +10,8 @@ import (
 	"path/filepath"
 	"strings"
 
+	rpc "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
+
 	user "github.com/cs3org/go-cs3apis/cs3/identity/user/v1beta1"
 	v1beta11 "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
 	provider "github.com/cs3org/go-cs3apis/cs3/storage/provider/v1beta1"
@@ -408,3 +410,25 @@ func (idx *NonUnique) getAuthenticatedContext(ctx context.Context) (context.Cont
 	ctx = metadata.AppendToOutgoingContext(ctx, token.TokenHeader, t)
 	return ctx, nil
 }
+
+// Delete deletes the index folder from its storage.
+func (idx *NonUnique) Delete() error {
+	ctx, err := idx.getAuthenticatedContext(context.Background())
+	if err != nil {
+		return err
+	}
+
+	res, err := idx.storageProvider.Delete(ctx, &provider.DeleteRequest{
+		Ref: &provider.Reference{
+			Spec: &provider.Reference_Path{Path: path.Join("/meta", idx.indexRootDir)},
+		},
+	})
+	if err != nil {
+		return err
+	}
+	if res.Status.Code != rpc.Code_CODE_OK {
+		return fmt.Errorf("error deleting index root dir: %v", idx.indexRootDir)
+	}
+
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/cs3/unique.go b/accounts/pkg/indexer/index/cs3/unique.go
index a5526b47c..9768eac6b 100644
--- a/accounts/pkg/indexer/index/cs3/unique.go
+++ b/accounts/pkg/indexer/index/cs3/unique.go
@@ -11,6 +11,7 @@ import (
 	"strings"
 
 	user "github.com/cs3org/go-cs3apis/cs3/identity/user/v1beta1"
+	rpc "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
 	v1beta11 "github.com/cs3org/go-cs3apis/cs3/rpc/v1beta1"
 	provider "github.com/cs3org/go-cs3apis/cs3/storage/provider/v1beta1"
 	"github.com/cs3org/reva/pkg/rgrpc/todo/pool"
@@ -370,3 +371,34 @@ func (idx *Unique) authenticate(ctx context.Context) (token string, err error) {
 	}
 	return idx.tokenManager.MintToken(ctx, u)
 }
+
+func (idx *Unique) getAuthenticatedContext(ctx context.Context) (context.Context, error) {
+	t, err := idx.authenticate(ctx)
+	if err != nil {
+		return nil, err
+	}
+	ctx = metadata.AppendToOutgoingContext(ctx, token.TokenHeader, t)
+	return ctx, nil
+}
+
+// Delete deletes the index folder from its storage.
+func (idx *Unique) Delete() error {
+	ctx, err := idx.getAuthenticatedContext(context.Background())
+	if err != nil {
+		return err
+	}
+
+	res, err := idx.storageProvider.Delete(ctx, &provider.DeleteRequest{
+		Ref: &provider.Reference{
+			Spec: &provider.Reference_Path{Path: path.Join("/meta", idx.indexRootDir)},
+		},
+	})
+	if err != nil {
+		return err
+	}
+	if res.Status.Code != rpc.Code_CODE_OK {
+		return fmt.Errorf("error deleting index root dir: %v", idx.indexRootDir)
+	}
+
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/disk/autoincrement.go b/accounts/pkg/indexer/index/disk/autoincrement.go
index 170e274b9..279b5edb8 100644
--- a/accounts/pkg/indexer/index/disk/autoincrement.go
+++ b/accounts/pkg/indexer/index/disk/autoincrement.go
@@ -19,11 +19,11 @@ import (
 
 // Autoincrement are fields for an index of type autoincrement.
 type Autoincrement struct {
-	indexBy         string
-	typeName        string
-	filesDir        string
-	indexBaseDir    string
-	indexRootDir    string
+	indexBy      string
+	typeName     string
+	filesDir     string
+	indexBaseDir string
+	indexRootDir string
 
 	bound *option.Bound
 }
@@ -54,12 +54,12 @@ func NewAutoincrementIndex(o ...option.Option) index.Index {
 	}
 
 	return &Autoincrement{
-		indexBy:         opts.IndexBy,
-		typeName:        opts.TypeName,
-		filesDir:        opts.FilesDir,
-		bound:           opts.Bound,
-		indexBaseDir:    path.Join(opts.DataDir, "index.disk"),
-		indexRootDir:    path.Join(path.Join(opts.DataDir, "index.disk"), strings.Join([]string{"autoincrement", opts.TypeName, opts.IndexBy}, ".")),
+		indexBy:      opts.IndexBy,
+		typeName:     opts.TypeName,
+		filesDir:     opts.FilesDir,
+		bound:        opts.Bound,
+		indexBaseDir: path.Join(opts.DataDir, "index.disk"),
+		indexRootDir: path.Join(path.Join(opts.DataDir, "index.disk"), strings.Join([]string{"autoincrement", opts.TypeName, opts.IndexBy}, ".")),
 	}
 }
 
@@ -260,3 +260,8 @@ func (idx *Autoincrement) next() (int, error) {
 
 	return latest + 1, nil
 }
+
+// Delete deletes the index folder from its storage.
+func (idx *Autoincrement) Delete() error {
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/disk/non_unique.go b/accounts/pkg/indexer/index/disk/non_unique.go
index 8f0c7d694..b4df3db5b 100644
--- a/accounts/pkg/indexer/index/disk/non_unique.go
+++ b/accounts/pkg/indexer/index/disk/non_unique.go
@@ -233,3 +233,8 @@ func (idx *NonUnique) TypeName() string {
 func (idx *NonUnique) FilesDir() string {
 	return idx.filesDir
 }
+
+// Delete deletes the index folder from its storage.
+func (idx *NonUnique) Delete() error {
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/disk/unique.go b/accounts/pkg/indexer/index/disk/unique.go
index 7b9436223..6a5374469 100644
--- a/accounts/pkg/indexer/index/disk/unique.go
+++ b/accounts/pkg/indexer/index/disk/unique.go
@@ -220,3 +220,8 @@ func isValidSymlink(path string) (err error) {
 
 	return
 }
+
+// Delete deletes the index folder from its storage.
+func (idx *Unique) Delete() error {
+	return nil
+}
diff --git a/accounts/pkg/indexer/index/index.go b/accounts/pkg/indexer/index/index.go
index e6f62862e..9ad7aee7b 100644
--- a/accounts/pkg/indexer/index/index.go
+++ b/accounts/pkg/indexer/index/index.go
@@ -13,4 +13,5 @@ type Index interface {
 	IndexBy() string
 	TypeName() string
 	FilesDir() string
+	Delete() error // Delete deletes the index folder from its storage.
 }
diff --git a/accounts/pkg/indexer/indexer.go b/accounts/pkg/indexer/indexer.go
index 01426e585..064ac6d75 100644
--- a/accounts/pkg/indexer/indexer.go
+++ b/accounts/pkg/indexer/indexer.go
@@ -43,11 +43,17 @@ func getRegistryStrategy(cfg *config.Config) string {
 }
 
 func (i Indexer) Reset() error {
-	for k := range i.indices {
-		delete(i.indices, k)
-	}
+	// TODO: is the root "index.cs3" folder somewhere?
+	// basically every implementation should take care of deleting its root folder.
 
-	// TODO: delete indexes from storage (cs3 / disk)
+	for j := range i.indices {
+		for _, indices := range i.indices[j].IndicesByField {
+			for _, idx := range indices {
+				_ = idx.Delete()
+			}
+		}
+		delete(i.indices, j)
+	}
 
 	return nil
 }
diff --git a/accounts/pkg/service/v0/index.go b/accounts/pkg/service/v0/index.go
index a0eeedce2..58517cb80 100644
--- a/accounts/pkg/service/v0/index.go
+++ b/accounts/pkg/service/v0/index.go
@@ -14,9 +14,8 @@ func (s Service) RebuildIndex(ctx context.Context, request *proto.RebuildIndexRe
 	if err := s.index.Reset(); err != nil {
 		return err
 	}
-	response.Indices = []string{"foo", "bar"}
 
-	if err := createIndices(s.index, s.Config); err != nil {
+	if err := recreateContainers(s.index, s.Config); err != nil {
 		return err
 	}
 
@@ -25,8 +24,8 @@ func (s Service) RebuildIndex(ctx context.Context, request *proto.RebuildIndexRe
 	return nil
 }
 
-// createIndices adds all indices to the indexer that we have for this service.
-func createIndices(idx *indexer.Indexer, cfg *config.Config) error {
+// recreateContainers adds all indices to the indexer that we have for this service.
+func recreateContainers(idx *indexer.Indexer, cfg *config.Config) error {
 	// Accounts
 	if err := idx.AddIndex(&proto.Account{}, "DisplayName", "Id", "accounts", "non_unique", nil, true); err != nil {
 		return err