diff --git a/pkg/networkserver/grpc_deviceregistry.go b/pkg/networkserver/grpc_deviceregistry.go
index c0e84fcfc9c..188e83b2431 100644
--- a/pkg/networkserver/grpc_deviceregistry.go
+++ b/pkg/networkserver/grpc_deviceregistry.go
@@ -2682,102 +2682,110 @@ func (ns *NetworkServer) Set(ctx context.Context, req *ttnpb.SetEndDeviceRequest
 	}
 
 	var evt events.Event
-	dev, ctx, err := ns.devices.SetByID(ctx, st.Device.Ids.ApplicationIds, st.Device.Ids.DeviceId, st.GetFields(), st.SetFunc(func(ctx context.Context, stored *ttnpb.EndDevice) error {
-		if hasSession {
-			macVersion := stored.GetMacState().GetLorawanVersion()
-			if stored.GetMacState() == nil && !st.HasSetField("mac_state") {
-				fps, err := ns.FrequencyPlansStore(ctx)
-				if err != nil {
+	dev, ctx, err := ns.devices.SetByID(
+		ctx, st.Device.Ids.ApplicationIds, st.Device.Ids.DeviceId, ttnpb.EndDeviceFieldPathsTopLevel, st.SetFunc(func(ctx context.Context, stored *ttnpb.EndDevice) error {
+			if nonZeroFields := ttnpb.NonZeroFields(stored, st.GetFields()...); len(nonZeroFields) > 0 {
+				newStored := &ttnpb.EndDevice{}
+				if err := newStored.SetFields(stored, nonZeroFields...); err != nil {
 					return err
 				}
-				macState, err := mac.NewState(st.Device, fps, ns.defaultMACSettings)
-				if err != nil {
-					return err
-				}
-				if macSets := ttnpb.FieldsWithoutPrefix("mac_state", st.SetFields()...); len(macSets) != 0 {
-					if err := macState.SetFields(st.Device.MacState, macSets...); err != nil {
+				stored = newStored
+			}
+			if hasSession {
+				macVersion := stored.GetMacState().GetLorawanVersion()
+				if stored.GetMacState() == nil && !st.HasSetField("mac_state") {
+					fps, err := ns.FrequencyPlansStore(ctx)
+					if err != nil {
+						return err
+					}
+					macState, err := mac.NewState(st.Device, fps, ns.defaultMACSettings)
+					if err != nil {
 						return err
 					}
+					if macSets := ttnpb.FieldsWithoutPrefix("mac_state", st.SetFields()...); len(macSets) != 0 {
+						if err := macState.SetFields(st.Device.MacState, macSets...); err != nil {
+							return err
+						}
+					}
+					st.Device.MacState = macState
+					st.AddSetFields(
+						"mac_state",
+					)
+					macVersion = macState.LorawanVersion
+				} else if st.HasSetField("mac_state.lorawan_version") {
+					macVersion = st.Device.MacState.LorawanVersion
+				}
+
+				if st.HasSetField("session.keys.f_nwk_s_int_key.key") && !macspec.UseNwkKey(macVersion) {
+					st.Device.Session.Keys.NwkSEncKey = st.Device.Session.Keys.FNwkSIntKey
+					st.Device.Session.Keys.SNwkSIntKey = st.Device.Session.Keys.FNwkSIntKey
+					st.AddSetFields(
+						"session.keys.nwk_s_enc_key.encrypted_key",
+						"session.keys.nwk_s_enc_key.kek_label",
+						"session.keys.nwk_s_enc_key.key",
+						"session.keys.s_nwk_s_int_key.encrypted_key",
+						"session.keys.s_nwk_s_int_key.kek_label",
+						"session.keys.s_nwk_s_int_key.key",
+					)
+				}
+				if st.HasSetField("session.started_at") && st.Device.GetSession().GetStartedAt() == nil ||
+					st.HasSetField("session.session_key_id") && !bytes.Equal(st.Device.GetSession().GetKeys().GetSessionKeyId(), stored.GetSession().GetKeys().GetSessionKeyId()) ||
+					stored.GetSession().GetStartedAt() == nil {
+					st.Device.Session.StartedAt = timestamppb.New(time.Now()) // NOTE: This is not equivalent to timestamppb.Now().
+					st.AddSetFields(
+						"session.started_at",
+					)
 				}
-				st.Device.MacState = macState
-				st.AddSetFields(
-					"mac_state",
-				)
-				macVersion = macState.LorawanVersion
-			} else if st.HasSetField("mac_state.lorawan_version") {
-				macVersion = st.Device.MacState.LorawanVersion
-			}
-
-			if st.HasSetField("session.keys.f_nwk_s_int_key.key") && !macspec.UseNwkKey(macVersion) {
-				st.Device.Session.Keys.NwkSEncKey = st.Device.Session.Keys.FNwkSIntKey
-				st.Device.Session.Keys.SNwkSIntKey = st.Device.Session.Keys.FNwkSIntKey
-				st.AddSetFields(
-					"session.keys.nwk_s_enc_key.encrypted_key",
-					"session.keys.nwk_s_enc_key.kek_label",
-					"session.keys.nwk_s_enc_key.key",
-					"session.keys.s_nwk_s_int_key.encrypted_key",
-					"session.keys.s_nwk_s_int_key.kek_label",
-					"session.keys.s_nwk_s_int_key.key",
-				)
-			}
-			if st.HasSetField("session.started_at") && st.Device.GetSession().GetStartedAt() == nil ||
-				st.HasSetField("session.session_key_id") && !bytes.Equal(st.Device.GetSession().GetKeys().GetSessionKeyId(), stored.GetSession().GetKeys().GetSessionKeyId()) ||
-				stored.GetSession().GetStartedAt() == nil {
-				st.Device.Session.StartedAt = timestamppb.New(time.Now()) // NOTE: This is not equivalent to timestamppb.Now().
-				st.AddSetFields(
-					"session.started_at",
-				)
 			}
-		}
-		if hasPendingSession {
-			var macVersion ttnpb.MACVersion
-			if st.HasSetField("pending_mac_state.lorawan_version") {
-				macVersion = st.Device.GetPendingMacState().GetLorawanVersion()
-			} else {
-				macVersion = stored.GetPendingMacState().GetLorawanVersion()
-			}
-
-			useNwkKey := macspec.UseNwkKey(macVersion)
-			if st.HasSetField("pending_session.keys.f_nwk_s_int_key.key") && !useNwkKey {
-				st.Device.PendingSession.Keys.NwkSEncKey = st.Device.PendingSession.Keys.FNwkSIntKey
-				st.Device.PendingSession.Keys.SNwkSIntKey = st.Device.PendingSession.Keys.FNwkSIntKey
-				st.AddSetFields(
-					"pending_session.keys.nwk_s_enc_key.encrypted_key",
-					"pending_session.keys.nwk_s_enc_key.kek_label",
-					"pending_session.keys.nwk_s_enc_key.key",
-					"pending_session.keys.s_nwk_s_int_key.encrypted_key",
-					"pending_session.keys.s_nwk_s_int_key.kek_label",
-					"pending_session.keys.s_nwk_s_int_key.key",
-				)
-			}
-			if st.HasSetField("pending_mac_state.queued_join_accept.keys.f_nwk_s_int_key.key") && hasQueuedJoinAccept && !useNwkKey {
-				st.Device.PendingMacState.QueuedJoinAccept.Keys.NwkSEncKey = st.Device.PendingMacState.QueuedJoinAccept.Keys.FNwkSIntKey
-				st.Device.PendingMacState.QueuedJoinAccept.Keys.SNwkSIntKey = st.Device.PendingMacState.QueuedJoinAccept.Keys.FNwkSIntKey
-				st.AddSetFields(
-					"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.encrypted_key",
-					"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.kek_label",
-					"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.key",
-					"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.encrypted_key",
-					"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.kek_label",
-					"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.key",
-				)
+			if hasPendingSession {
+				var macVersion ttnpb.MACVersion
+				if st.HasSetField("pending_mac_state.lorawan_version") {
+					macVersion = st.Device.GetPendingMacState().GetLorawanVersion()
+				} else {
+					macVersion = stored.GetPendingMacState().GetLorawanVersion()
+				}
+
+				useNwkKey := macspec.UseNwkKey(macVersion)
+				if st.HasSetField("pending_session.keys.f_nwk_s_int_key.key") && !useNwkKey {
+					st.Device.PendingSession.Keys.NwkSEncKey = st.Device.PendingSession.Keys.FNwkSIntKey
+					st.Device.PendingSession.Keys.SNwkSIntKey = st.Device.PendingSession.Keys.FNwkSIntKey
+					st.AddSetFields(
+						"pending_session.keys.nwk_s_enc_key.encrypted_key",
+						"pending_session.keys.nwk_s_enc_key.kek_label",
+						"pending_session.keys.nwk_s_enc_key.key",
+						"pending_session.keys.s_nwk_s_int_key.encrypted_key",
+						"pending_session.keys.s_nwk_s_int_key.kek_label",
+						"pending_session.keys.s_nwk_s_int_key.key",
+					)
+				}
+				if st.HasSetField("pending_mac_state.queued_join_accept.keys.f_nwk_s_int_key.key") && hasQueuedJoinAccept && !useNwkKey {
+					st.Device.PendingMacState.QueuedJoinAccept.Keys.NwkSEncKey = st.Device.PendingMacState.QueuedJoinAccept.Keys.FNwkSIntKey
+					st.Device.PendingMacState.QueuedJoinAccept.Keys.SNwkSIntKey = st.Device.PendingMacState.QueuedJoinAccept.Keys.FNwkSIntKey
+					st.AddSetFields(
+						"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.encrypted_key",
+						"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.kek_label",
+						"pending_mac_state.queued_join_accept.keys.nwk_s_enc_key.key",
+						"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.encrypted_key",
+						"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.kek_label",
+						"pending_mac_state.queued_join_accept.keys.s_nwk_s_int_key.key",
+					)
+				}
 			}
-		}
 
-		if stored == nil {
-			evt = evtCreateEndDevice.NewWithIdentifiersAndData(ctx, st.Device.Ids, nil)
-			return nil
-		}
+			if stored == nil {
+				evt = evtCreateEndDevice.NewWithIdentifiersAndData(ctx, st.Device.Ids, nil)
+				return nil
+			}
 
-		evt = evtUpdateEndDevice.NewWithIdentifiersAndData(ctx, st.Device.Ids, req.FieldMask.GetPaths())
-		if st.HasSetField("multicast") && st.Device.Multicast != stored.Multicast {
-			return newInvalidFieldValueError("multicast")
-		}
-		if st.HasSetField("supports_join") && st.Device.SupportsJoin != stored.SupportsJoin {
-			return newInvalidFieldValueError("supports_join")
-		}
-		return nil
-	}))
+			evt = evtUpdateEndDevice.NewWithIdentifiersAndData(ctx, st.Device.Ids, req.FieldMask.GetPaths())
+			if st.HasSetField("multicast") && st.Device.Multicast != stored.Multicast {
+				return newInvalidFieldValueError("multicast")
+			}
+			if st.HasSetField("supports_join") && st.Device.SupportsJoin != stored.SupportsJoin {
+				return newInvalidFieldValueError("supports_join")
+			}
+			return nil
+		}))
 	if err != nil {
 		logRegistryRPCError(ctx, err, "Failed to set device in registry")
 		return nil, err