diff --git a/server/pkg/publisher/interface.go b/server/pkg/publisher/interface.go
index d1d27577..2eb3de11 100644
--- a/server/pkg/publisher/interface.go
+++ b/server/pkg/publisher/interface.go
@@ -30,4 +30,5 @@ type RepositoryInterface interface {
 	StageTarget(ctx context.Context, pathInsideTargets string, data io.Reader) error
 	CommitStaged(ctx context.Context) error
 	GetTargets(ctx context.Context) ([]string, error)
+	GetRolePublicKeysFromS3Meta(file, role string) ([]string, error)
 }
diff --git a/server/pkg/publisher/publisher.go b/server/pkg/publisher/publisher.go
index ff0a133f..a9e74538 100644
--- a/server/pkg/publisher/publisher.go
+++ b/server/pkg/publisher/publisher.go
@@ -3,12 +3,14 @@ package publisher
 import (
 	"bytes"
 	"context"
+	"encoding/json"
 	"errors"
 	"fmt"
 	"io"
 	"os"
 	"path"
 	"path/filepath"
+	"slices"
 	"strings"
 	"sync"
 	"unicode/utf8"
@@ -18,6 +20,7 @@ import (
 	"github.com/hashicorp/go-hclog"
 	"github.com/hashicorp/vault/sdk/logical"
 
+	"github.com/werf/logboek"
 	"github.com/werf/trdl/server/pkg/config"
 	"github.com/werf/trdl/server/pkg/pgp"
 	"github.com/werf/trdl/server/pkg/util"
@@ -94,6 +97,9 @@ type setRepositoryKeysOptions struct {
 	InitializeKeys bool
 }
 
+var TufRepoAlreadyInitializedMsg = `Tuf repository already initialized by another instance of vault-plugin. 
+Verify the project settings. If settings are correct, consider cleaning up the TUF repository by removing orphaned metadata.`
+
 func (publisher *Publisher) setRepositoryKeys(ctx context.Context, storage logical.Storage, repository RepositoryInterface, opts setRepositoryKeysOptions) error {
 	entry, err := storage.Get(ctx, storageKeyTufRepositoryKeys)
 	if err != nil {
@@ -105,6 +111,16 @@ func (publisher *Publisher) setRepositoryKeys(ctx context.Context, storage logic
 			return ErrUninitializedRepositoryKeys
 		}
 
+		rootPublicKeysFromS3, err := repository.GetRolePublicKeysFromS3Meta("root.json", "root")
+		if err != nil {
+			return fmt.Errorf("unable to get root keys from repository: %w", err)
+		}
+		if len(rootPublicKeysFromS3) > 0 {
+			publisher.logger.Error(TufRepoAlreadyInitializedMsg)
+			logboek.Context(context.Background()).Default().LogF("%s\n", TufRepoAlreadyInitializedMsg)
+			return fmt.Errorf("tuf repository already initialized by another instance of vault-plugin")
+		}
+
 		publisher.logger.Debug("Will generate new repository private keys")
 
 		if err := repository.GenPrivKeys(); err != nil {
@@ -132,6 +148,24 @@ func (publisher *Publisher) setRepositoryKeys(ctx context.Context, storage logic
 		return fmt.Errorf("unable to decode keys json by the %q storage key:\n%s---\n%w", storageKeyTufRepositoryKeys, entry.Value, err)
 	}
 
+	rootPublicKeysFromS3, err := repository.GetRolePublicKeysFromS3Meta("root.json", "root")
+	if err != nil {
+		return fmt.Errorf("unable to get root keys from repository: %w", err)
+	}
+
+	var data KeyVal
+	if err := json.Unmarshal(privKeys.Root.Value, &data); err != nil {
+		return err
+	}
+
+	if len(rootPublicKeysFromS3) > 0 {
+		if !slices.Contains(rootPublicKeysFromS3, data.Public) {
+			publisher.logger.Error(TufRepoAlreadyInitializedMsg)
+			logboek.Context(context.Background()).Default().LogF("%s\n", TufRepoAlreadyInitializedMsg)
+			return fmt.Errorf("tuf repository already initialized by another instance of vault-plugin")
+		}
+	}
+
 	if err := repository.SetPrivKeys(privKeys); err != nil {
 		return fmt.Errorf("unable to set private keys into repository: %w", err)
 	}
diff --git a/server/pkg/publisher/repository.go b/server/pkg/publisher/repository.go
index abb36a0e..43636d06 100644
--- a/server/pkg/publisher/repository.go
+++ b/server/pkg/publisher/repository.go
@@ -160,3 +160,51 @@ func (repository *S3Repository) GetTargets(ctx context.Context) ([]string, error
 	}
 	return res, nil
 }
+
+type RootMeta struct {
+	Signed Signed `json:"signed"`
+}
+type Signed struct {
+	Keys  map[string]Key            `json:"keys"`
+	Roles map[string]RoleDefinition `json:"roles"`
+}
+
+type Key struct {
+	KeyVal KeyVal `json:"keyval"`
+}
+
+type KeyVal struct {
+	Public string `json:"public"`
+}
+
+type RoleDefinition struct {
+	KeyIDs []string `json:"keyids"`
+}
+
+func (repository *S3Repository) GetRolePublicKeysFromS3Meta(file, role string) ([]string, error) {
+	meta, err := repository.TufRepo.GetMeta()
+	if err != nil {
+		return nil, fmt.Errorf("error getting metadata from TUF repo: %w", err)
+	}
+
+	var rootMeta RootMeta
+	if err := json.Unmarshal(meta[file], &rootMeta); err != nil {
+		return nil, fmt.Errorf("error unmarshalling %s: %w", file, err)
+	}
+
+	rootRole, ok := rootMeta.Signed.Roles[role]
+	if !ok {
+		return nil, nil
+	}
+
+	publicKeys := make([]string, 0, len(rootRole.KeyIDs))
+	for _, keyID := range rootRole.KeyIDs {
+		key, ok := rootMeta.Signed.Keys[keyID]
+		if !ok {
+			return nil, fmt.Errorf("key %q not found in keys section", keyID)
+		}
+		publicKeys = append(publicKeys, key.KeyVal.Public)
+	}
+
+	return publicKeys, nil
+}