diff --git a/server/control/server.go b/server/control/server.go
index 131d116..ea32f64 100644
--- a/server/control/server.go
+++ b/server/control/server.go
@@ -30,6 +30,10 @@ func NewServer(cfg Config) (*Server, error) {
 		return nil, fmt.Errorf("config store open: %w", err)
 	}
 
+	if err := cfg.Stores.RemoveDeprecated(); err != nil {
+		cfg.Logger.Warn("could not remove deprecated stores", "err", err)
+	}
+
 	relays, err := newRelayServer(cfg.RelaysIngress, cfg.RelaysAuth, configStore, cfg.Stores, cfg.Logger)
 	if err != nil {
 		return nil, fmt.Errorf("create relay server: %w", err)
diff --git a/server/control/store.go b/server/control/store.go
index 4454e88..0638047 100644
--- a/server/control/store.go
+++ b/server/control/store.go
@@ -3,6 +3,8 @@ package control
 import (
 	"crypto/x509"
 	"encoding/json"
+	"errors"
+	"os"
 	"path/filepath"
 
 	"github.com/connet-dev/connet/model"
@@ -17,6 +19,8 @@ type Stores interface {
 	ClientPeers() (logc.KV[ClientPeerKey, ClientPeerValue], error)
 
 	RelayDirects() (logc.KV[RelayConnKey, RelayDirectValue], error)
+
+	RemoveDeprecated() error
 }
 
 func NewFileStores(dir string) Stores {
@@ -43,6 +47,16 @@ func (f *fileStores) RelayDirects() (logc.KV[RelayConnKey, RelayDirectValue], er
 	return logc.NewKV[RelayConnKey, RelayDirectValue](filepath.Join(f.dir, "relay-directs"))
 }
 
+func (f *fileStores) RemoveDeprecated() error {
+	return errors.Join(
+		os.RemoveAll(filepath.Join(f.dir, "relay-conns")),
+		os.RemoveAll(filepath.Join(f.dir, "relay-clients")),
+		os.RemoveAll(filepath.Join(f.dir, "relay-endpoints")),
+		os.RemoveAll(filepath.Join(f.dir, "relay-servers")),
+		os.RemoveAll(filepath.Join(f.dir, "relay-server-offsets")),
+	)
+}
+
 type ConfigKey string
 
 var (
diff --git a/server/relay/server.go b/server/relay/server.go
index ab63713..459c6e0 100644
--- a/server/relay/server.go
+++ b/server/relay/server.go
@@ -47,6 +47,10 @@ func NewServer(cfg Config) (*Server, error) {
 		return nil, fmt.Errorf("relay stores: %w", err)
 	}
 
+	if err := cfg.Stores.RemoveDeprecated(); err != nil {
+		cfg.Logger.Warn("could not remove deprecated stores", "err", err)
+	}
+
 	statelessResetVal, err := configStore.GetOrInit(configStatelessReset, func(ck ConfigKey) (ConfigValue, error) {
 		var key quic.StatelessResetKey
 		if _, err := io.ReadFull(rand.Reader, key[:]); err != nil {
diff --git a/server/relay/store.go b/server/relay/store.go
index e0ed1bc..e8e7f07 100644
--- a/server/relay/store.go
+++ b/server/relay/store.go
@@ -1,19 +1,17 @@
 package relay
 
 import (
-	"crypto/x509"
-	"encoding/json"
+	"errors"
+	"os"
 	"path/filepath"
 
-	"github.com/connet-dev/connet/model"
-	"github.com/connet-dev/connet/pkg/certc"
 	"github.com/connet-dev/connet/pkg/logc"
 )
 
 type Stores interface {
 	Config() (logc.KV[ConfigKey, ConfigValue], error)
-	Clients() (logc.KV[ClientKey, ClientValue], error)
-	Servers() (logc.KV[ServerKey, ServerValue], error)
+
+	RemoveDeprecated() error
 }
 
 func NewFileStores(dir string) Stores {
@@ -28,12 +26,11 @@ func (f *fileStores) Config() (logc.KV[ConfigKey, ConfigValue], error) {
 	return logc.NewKV[ConfigKey, ConfigValue](filepath.Join(f.dir, "config"))
 }
 
-func (f *fileStores) Clients() (logc.KV[ClientKey, ClientValue], error) {
-	return logc.NewKV[ClientKey, ClientValue](filepath.Join(f.dir, "clients"))
-}
-
-func (f *fileStores) Servers() (logc.KV[ServerKey, ServerValue], error) {
-	return logc.NewKV[ServerKey, ServerValue](filepath.Join(f.dir, "servers"))
+func (f *fileStores) RemoveDeprecated() error {
+	return errors.Join(
+		os.RemoveAll(filepath.Join(f.dir, "clients")),
+		os.RemoveAll(filepath.Join(f.dir, "servers")),
+	)
 }
 
 type ConfigKey string
@@ -49,104 +46,3 @@ type ConfigValue struct {
 	String string `json:"string,omitempty"`
 	Bytes  []byte `json:"bytes,omitempty"`
 }
-
-type ClientKey struct {
-	Endpoint model.Endpoint `json:"endpoint"`
-	Role     model.Role     `json:"role"`
-	Key      model.Key      `json:"key"`
-}
-
-type ClientValue struct {
-	Cert *x509.Certificate `json:"cert"`
-}
-
-func (v ClientValue) MarshalJSON() ([]byte, error) {
-	return certc.MarshalJSONCert(v.Cert)
-}
-
-func (v *ClientValue) UnmarshalJSON(b []byte) error {
-	cert, err := certc.UnmarshalJSONCert(b)
-	if err != nil {
-		return err
-	}
-
-	*v = ClientValue{cert}
-	return nil
-}
-
-type ServerKey struct {
-	Endpoint model.Endpoint `json:"endpoint"`
-}
-
-type ServerValue struct {
-	Name    string                          `json:"name"`
-	Cert    *certc.Cert                     `json:"cert"`
-	Clients map[serverClientKey]ClientValue `json:"clients"`
-}
-
-func (v ServerValue) MarshalJSON() ([]byte, error) {
-	cert, key, err := v.Cert.EncodeToMemory()
-	if err != nil {
-		return nil, err
-	}
-
-	s := struct {
-		Name    string              `json:"name"`
-		Cert    []byte              `json:"cert"`
-		CertKey []byte              `json:"cert_key"`
-		Clients []serverClientValue `json:"clients"`
-	}{
-		Name:    v.Name,
-		Cert:    cert,
-		CertKey: key,
-	}
-
-	for k, v := range v.Clients {
-		s.Clients = append(s.Clients, serverClientValue{
-			Role:  k.Role,
-			Value: v,
-		})
-	}
-
-	return json.Marshal(s)
-}
-
-func (v *ServerValue) UnmarshalJSON(b []byte) error {
-	s := struct {
-		Name    string              `json:"name"`
-		Cert    []byte              `json:"cert"`
-		CertKey []byte              `json:"cert_key"`
-		Clients []serverClientValue `json:"clients"`
-	}{}
-	if err := json.Unmarshal(b, &s); err != nil {
-		return err
-	}
-
-	cert, err := certc.DecodeFromMemory(s.Cert, s.CertKey)
-	if err != nil {
-		return err
-	}
-
-	sv := ServerValue{
-		Name:    s.Name,
-		Cert:    cert,
-		Clients: map[serverClientKey]ClientValue{},
-	}
-
-	for _, cl := range s.Clients {
-		sv.Clients[serverClientKey{cl.Role, model.NewKey(cl.Value.Cert)}] = cl.Value
-	}
-
-	*v = sv
-	return nil
-}
-
-type serverClientKey struct {
-	Role model.Role `json:"role"`
-	Key  model.Key  `json:"key"`
-}
-
-type serverClientValue struct {
-	Role  model.Role  `json:"role"`
-	Value ClientValue `json:"value"`
-}