diff --git a/CHANGELOG.md b/CHANGELOG.md
index d8b75d4fee..2ef3c81b46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,12 +8,26 @@ Changelog for NeoFS Node
 ### Fixed
 
 ### Changed
+- Move `fschain_autodeploy` into `fschain.disable_autodeploy` in IR config (#3619)
+- Move `without_mainnet` into `mainnet.enabled` in IR config (#3619)
+- Move `governance.disable` into `mainnet.disable_governance_sync` in IR config (#3619)
+- Move `fee.main_chain` into `mainnet.extra_fee` in IR config (#3619)
+- Move `contracts` into `mainnet.contracts` in IR config (#3619)
 
 ### Removed
 
 ### Updated
 
 ### Updating from v0.49.0
+Use IR configuration options:
+- `fschain.disable_autodeploy` instead of deprecated `fschain_autodeploy` with reverted value,
+by default autodeploy is enabled now;
+- `mainnet.enabled` instead of deprecated `without_mainnet` with reverted value,
+by default mainnet is disabled now;
+- `mainnet.disable_governance_sync` instead of deprecated `governance.disable`;
+- `mainnet.extra_fee` instead of deprecated `fee.main_chain`;
+- `mainnet.contracts` instead of deprecated `contracts`;
+Old options are still supported but will be removed in future releases.
 
 ## [0.49.0] - 2025-10-06 - Dochodo
 
diff --git a/cmd/neofs-ir/defaults.go b/cmd/neofs-ir/defaults.go
index bacbf868cc..5c08ab5597 100644
--- a/cmd/neofs-ir/defaults.go
+++ b/cmd/neofs-ir/defaults.go
@@ -5,6 +5,7 @@ import (
 	"strings"
 	"time"
 
+	"github.com/nspcc-dev/neo-go/pkg/crypto/keys"
 	"github.com/nspcc-dev/neofs-node/internal/configutil"
 	irconfig "github.com/nspcc-dev/neofs-node/pkg/innerring/config"
 	"github.com/spf13/viper"
@@ -22,8 +23,6 @@ func newConfig(path string) (*irconfig.Config, error) {
 	v.AutomaticEnv()
 	v.SetEnvKeyReplacer(strings.NewReplacer(".", "_"))
 
-	defaultConfiguration(v)
-
 	if path != "" {
 		v.SetConfigFile(path)
 		if strings.HasSuffix(path, ".json") {
@@ -43,61 +42,115 @@ func newConfig(path string) (*irconfig.Config, error) {
 		return nil, fmt.Errorf("unable to decode config: %w", err)
 	}
 
+	applyDefaults(&cfg)
+
 	return &cfg, nil
 }
 
-func defaultConfiguration(cfg *viper.Viper) {
-	cfg.SetDefault("logger.level", "info")
-	cfg.SetDefault("logger.encoding", "console")
-
-	cfg.SetDefault("pprof.address", "localhost:6060")
-	cfg.SetDefault("pprof.shutdown_timeout", "30s")
-
-	cfg.SetDefault("prometheus.address", "localhost:9090")
-	cfg.SetDefault("prometheus.shutdown_timeout", "30s")
-
-	cfg.SetDefault("without_mainnet", false)
-
-	cfg.SetDefault("node.persistent_state.path", ".neofs-ir-state")
-
-	cfg.SetDefault("fschain.dial_timeout", time.Minute)
-	cfg.SetDefault("fschain.reconnections_number", 5)
-	cfg.SetDefault("fschain.reconnections_delay", 5*time.Second)
-	cfg.SetDefault("fschain.validators", []string{})
+func applyDefaults(cfg *irconfig.Config) {
+	// Logger defaults
+	if cfg.Logger.Level == "" {
+		cfg.Logger.Level = "info"
+	}
+	if cfg.Logger.Encoding == "" {
+		cfg.Logger.Encoding = "console"
+	}
 
-	cfg.SetDefault("mainnet.dial_timeout", time.Minute)
-	cfg.SetDefault("mainnet.reconnections_number", 5)
-	cfg.SetDefault("mainnet.reconnections_delay", 5*time.Second)
+	// Pprof defaults
+	if cfg.Pprof.Address == "" {
+		cfg.Pprof.Address = "localhost:6060"
+	}
+	if cfg.Pprof.ShutdownTimeout == 0 {
+		cfg.Pprof.ShutdownTimeout = 30 * time.Second
+	}
 
-	cfg.SetDefault("wallet.path", "")     // inner ring node NEP-6 wallet
-	cfg.SetDefault("wallet.address", "")  // account address
-	cfg.SetDefault("wallet.password", "") // password
+	// Prometheus defaults
+	if cfg.Prometheus.Address == "" {
+		cfg.Prometheus.Address = "localhost:9090"
+	}
+	if cfg.Prometheus.ShutdownTimeout == 0 {
+		cfg.Prometheus.ShutdownTimeout = 30 * time.Second
+	}
 
-	cfg.SetDefault("timers.collect_basic_income.mul", 1)
-	cfg.SetDefault("timers.collect_basic_income.div", 2)
+	// Node defaults
+	if cfg.Node.PersistentState.Path == "" {
+		cfg.Node.PersistentState.Path = ".neofs-ir-state"
+	}
 
-	cfg.SetDefault("workers.netmap", "10")
-	cfg.SetDefault("workers.balance", "10")
-	cfg.SetDefault("workers.neofs", "10")
-	cfg.SetDefault("workers.container", "10")
-	cfg.SetDefault("workers.alphabet", "10")
-	cfg.SetDefault("workers.reputation", "10")
+	// FSChain defaults
+	if cfg.FSChain.DialTimeout == 0 {
+		cfg.FSChain.DialTimeout = time.Minute
+	}
+	if cfg.FSChain.ReconnectionsNumber == 0 {
+		cfg.FSChain.ReconnectionsNumber = 5
+	}
+	if cfg.FSChain.ReconnectionsDelay == 0 {
+		cfg.FSChain.ReconnectionsDelay = 5 * time.Second
+	}
+	if cfg.FSChain.Validators == nil {
+		cfg.FSChain.Validators = keys.PublicKeys{}
+	}
 
-	cfg.SetDefault("emit.storage.amount", 0)
-	cfg.SetDefault("emit.mint.cache_size", 1000)
-	cfg.SetDefault("emit.mint.threshold", 1)
-	cfg.SetDefault("emit.mint.value", 20000000) // 0.2 Fixed8
-	cfg.SetDefault("emit.gas.balance_threshold", 0)
+	// Mainnet defaults
+	if cfg.Mainnet.ExtraFee == 0 {
+		cfg.Mainnet.ExtraFee = 5000_0000 // 0.5 Fixed8
+	}
+	if cfg.Mainnet.DialTimeout == 0 {
+		cfg.Mainnet.DialTimeout = time.Minute
+	}
+	if cfg.Mainnet.ReconnectionsNumber == 0 {
+		cfg.Mainnet.ReconnectionsNumber = 5
+	}
+	if cfg.Mainnet.ReconnectionsDelay == 0 {
+		cfg.Mainnet.ReconnectionsDelay = 5 * time.Second
+	}
 
-	cfg.SetDefault("settlement.basic_income_rate", 0)
+	// Timers defaults
+	if cfg.Timers.CollectBasicIncome.Mul == 0 {
+		cfg.Timers.CollectBasicIncome.Mul = 1
+	}
+	if cfg.Timers.CollectBasicIncome.Div == 0 {
+		cfg.Timers.CollectBasicIncome.Div = 2
+	}
 
-	cfg.SetDefault("indexer.cache_timeout", 15*time.Second)
+	// Workers defaults
+	if cfg.Workers.Netmap == 0 {
+		cfg.Workers.Netmap = 10
+	}
+	if cfg.Workers.Balance == 0 {
+		cfg.Workers.Balance = 10
+	}
+	if cfg.Workers.NeoFS == 0 {
+		cfg.Workers.NeoFS = 10
+	}
+	if cfg.Workers.Container == 0 {
+		cfg.Workers.Container = 10
+	}
+	if cfg.Workers.Alphabet == 0 {
+		cfg.Workers.Alphabet = 10
+	}
+	if cfg.Workers.Reputation == 0 {
+		cfg.Workers.Reputation = 10
+	}
 
-	// extra fee values for working mode without notary contract
-	cfg.SetDefault("fee.main_chain", 5000_0000) // 0.5 Fixed8
+	// Emit defaults
+	if cfg.Emit.Mint.CacheSize == 0 {
+		cfg.Emit.Mint.CacheSize = 1000
+	}
+	if cfg.Emit.Mint.Threshold == 0 {
+		cfg.Emit.Mint.Threshold = 1
+	}
+	if cfg.Emit.Mint.Value == 0 {
+		cfg.Emit.Mint.Value = 20000000 // 0.2 Fixed8
+	}
 
-	cfg.SetDefault("control.authorized_keys", []string{})
-	cfg.SetDefault("control.grpc.endpoint", "")
+	// Indexer defaults
+	if cfg.Indexer.CacheTimeout == 0 {
+		cfg.Indexer.CacheTimeout = 15 * time.Second
+	}
 
-	cfg.SetDefault("governance.disable", false)
+	// Control defaults
+	if cfg.Control.AuthorizedKeys == nil {
+		cfg.Control.AuthorizedKeys = keys.PublicKeys{}
+	}
 }
diff --git a/cmd/neofs-ir/defaults_test.go b/cmd/neofs-ir/defaults_test.go
index 6c06d63fd2..6ee74c47d1 100644
--- a/cmd/neofs-ir/defaults_test.go
+++ b/cmd/neofs-ir/defaults_test.go
@@ -26,14 +26,23 @@ func TestValidateDefaultConfig(t *testing.T) {
 				ReconnectionsNumber: 5,
 				ReconnectionsDelay:  5000000000,
 			},
-			Validators: keys.PublicKeys{},
+			DisableAutodeploy: false,
+			Validators:        keys.PublicKeys{},
 		},
-		FSChainAutodeploy: false,
-		NNS:               config.NNS{SystemEmail: ""},
-		Mainnet: config.BasicChain{
-			DialTimeout:         60000000000,
-			ReconnectionsNumber: 5,
-			ReconnectionsDelay:  5000000000,
+		NNS: config.NNS{SystemEmail: ""},
+		Mainnet: config.Mainnet{
+			Enabled:               false,
+			DisableGovernanceSync: false,
+			ExtraFee:              50000000,
+			Contracts: config.Contracts{
+				NeoFS:      "",
+				Processing: "",
+			},
+			BasicChain: config.BasicChain{
+				DialTimeout:         60000000000,
+				ReconnectionsNumber: 5,
+				ReconnectionsDelay:  5000000000,
+			},
 		},
 		Control: config.Control{
 			AuthorizedKeys: keys.PublicKeys{},
@@ -45,7 +54,6 @@ func TestValidateDefaultConfig(t *testing.T) {
 				Path: ".neofs-ir-state",
 			},
 		},
-		Fee: config.Fee{MainChain: 50000000},
 		Timers: config.Timers{
 			CollectBasicIncome: config.BasicTimer{Mul: 1, Div: 2},
 		},
diff --git a/cmd/neofs-ir/validate_test.go b/cmd/neofs-ir/validate_test.go
index 98d24b9b1d..f92742d2a5 100644
--- a/cmd/neofs-ir/validate_test.go
+++ b/cmd/neofs-ir/validate_test.go
@@ -192,7 +192,8 @@ func TestCheckForUnknownFieldsExample(t *testing.T) {
 					"wss://sidechain2.fs.neo.org:30333/ws",
 				},
 			},
-			Validators: validators,
+			DisableAutodeploy: true,
+			Validators:        validators,
 			Consensus: config.Consensus{
 				Magic:     15405,
 				Committee: committee,
@@ -248,17 +249,25 @@ func TestCheckForUnknownFieldsExample(t *testing.T) {
 				RemoveUntraceableBlocks:         false,
 				P2PNotaryRequestPayloadPoolSize: 100,
 			}},
-		FSChainAutodeploy: true,
 		NNS: config.NNS{
 			SystemEmail: "usr@domain.io",
 		},
-		Mainnet: config.BasicChain{
-			DialTimeout:         time.Minute,
-			ReconnectionsNumber: 5,
-			ReconnectionsDelay:  5 * time.Second,
-			Endpoints: []string{
-				"wss://mainchain1.fs.neo.org:30333/ws",
-				"wss://mainchain.fs.neo.org:30333/ws",
+		Mainnet: config.Mainnet{
+			Enabled:               false,
+			DisableGovernanceSync: false,
+			ExtraFee:              50000000,
+			Contracts: config.Contracts{
+				NeoFS:      "ee3dee6d05dc79c24a5b8f6985e10d68b7cacc62",
+				Processing: "597f5894867113a41e192801709c02497f611de8",
+			},
+			BasicChain: config.BasicChain{
+				DialTimeout:         time.Minute,
+				ReconnectionsNumber: 5,
+				ReconnectionsDelay:  5 * time.Second,
+				Endpoints: []string{
+					"wss://mainchain1.fs.neo.org:30333/ws",
+					"wss://mainchain.fs.neo.org:30333/ws",
+				},
 			},
 		},
 		Control: config.Control{
diff --git a/config/example/ir.env b/config/example/ir.env
index 091395adb1..48bbae5b5c 100644
--- a/config/example/ir.env
+++ b/config/example/ir.env
@@ -8,12 +8,18 @@ NEOFS_IR_WALLET_PASSWORD=secret
 
 NEOFS_IR_WITHOUT_MAINNET=false
 
+NEOFS_IR_FSCHAIN_DISABLE_AUTODEPLOY=true
 NEOFS_IR_FSCHAIN_DIAL_TIMEOUT=1m
 NEOFS_IR_FSCHAIN_RECONNECTIONS_NUMBER=5
 NEOFS_IR_FSCHAIN_RECONNECTIONS_DELAY=5s
 NEOFS_IR_FSCHAIN_ENDPOINTS="wss://sidechain1.fs.neo.org:30333/ws wss://sidechain2.fs.neo.org:30333/ws"
 NEOFS_IR_FSCHAIN_VALIDATORS="0283120f4c8c1fc1d792af5063d2def9da5fddc90bc1384de7fcfdda33c3860170"
 
+NEOFS_IR_MAINNET_ENABLED=false
+NEOFS_IR_MAINNET_DISABLE_GOVERNANCE_SYNC=false
+NEOFS_IR_MAINNET_EXTRA_FEE=50000000
+NEOFS_IR_MAINNET_CONTRACTS_NEOFS=ee3dee6d05dc79c24a5b8f6985e10d68b7cacc62
+NEOFS_IR_MAINNET_CONTRACTS_PROCESSING=597f5894867113a41e192801709c02497f611de8MAINNET_
 NEOFS_IR_MAINNET_DIAL_TIMEOUT=1m
 NEOFS_IR_MAINNET_RECONNECTIONS_NUMBER=5
 NEOFS_IR_MAINNET_RECONNECTIONS_DELAY=5s
diff --git a/config/example/ir.yaml b/config/example/ir.yaml
index 99d7191da2..e2ac741786 100644
--- a/config/example/ir.yaml
+++ b/config/example/ir.yaml
@@ -16,6 +16,7 @@ wallet:
 without_mainnet: false # Run application in single chain environment without mainchain
 
 fschain:
+  disable_autodeploy: true # Optional flag to disable auto-deployment procedure of the FS chain; defaults to 'false'
   dial_timeout: 1m # Timeout for RPC client connection to sidechain
   reconnections_number: 5  # number of reconnection attempts
   reconnections_delay: 5s  # time delay b/w reconnection attempts
@@ -109,8 +110,7 @@ fschain:
     p2p_notary_request_payload_pool_size: 100 # Optional size of the node's P2P Notary request payloads memory pool.
     # Defaults to 1000. Must be unsigned integer in range [1:2147483647].
 
-fschain_autodeploy: true # Optional flag to run auto-deployment procedure of the FS chain. By default,
-  # the chain is expected to be deployed/updated in the background (e.g. via NeoFS ADM tool).
+fschain_autodeploy: false # Optional flag to run auto-deployment procedure of the FS chain. By default, 'true'.
   # If set, must be 'true' or 'false'.
 
 nns: # Optional configuration of the NNS domains processed during the FS chain deployment
@@ -118,6 +118,15 @@ nns: # Optional configuration of the NNS domains processed during the FS chain d
     # Defaults to 'nonexistent@nspcc.io'
 
 mainnet:
+  enabled: false # Enable connection to mainchain; by default, 'false', run application in single chain environment
+    # without mainchain; value revert deprecated 'without_mainnet'
+  disable_governance_sync: false # Disable synchronization of sidechain committee and mainchain role management contract;
+    # ignore if mainchain is disabled; same as 'governance.disable'
+  extra_fee: 50000000 # Fixed8 value of extra GAS fee for mainchain contract invocation; ignore if notary is enabled in mainchain;
+    # same as 'fee.main_chain'
+  contracts: # same as 'contracts'
+    neofs: ee3dee6d05dc79c24a5b8f6985e10d68b7cacc62      # Address of NeoFS contract in mainchain; ignore if mainchain is disabled
+    processing: 597f5894867113a41e192801709c02497f611de8 # Address of processing contract in mainchain; ignore if mainchain is disabled
   dial_timeout: 1m # Timeout for RPC client connection to mainchain; ignore if mainchain is disabled
   reconnections_number: 5  # number of reconnection attempts
   reconnections_delay: 5s  # time delay b/w reconnection attempts
diff --git a/pkg/innerring/config/config.go b/pkg/innerring/config/config.go
index 3ff915c096..78042f8bd9 100644
--- a/pkg/innerring/config/config.go
+++ b/pkg/innerring/config/config.go
@@ -22,7 +22,7 @@ type Config struct {
 
 	NNS NNS `mapstructure:"nns"`
 
-	Mainnet BasicChain `mapstructure:"mainnet"`
+	Mainnet Mainnet `mapstructure:"mainnet"`
 
 	Control Control `mapstructure:"control"`
 
@@ -131,6 +131,15 @@ type Experimental struct {
 	ChainMetaData bool `mapstructure:"chain_meta_data"`
 }
 
+// Mainnet configures mainnet chain settings.
+type Mainnet struct {
+	Enabled               bool      `mapstructure:"enabled"`
+	DisableGovernanceSync bool      `mapstructure:"disable_governance_sync"`
+	ExtraFee              int64     `mapstructure:"extra_fee"`
+	Contracts             Contracts `mapstructure:"contracts"`
+	BasicChain            `mapstructure:",squash"`
+}
+
 // IsSet checks if the key is set in the config.
 func (c *Config) IsSet(key string) bool {
 	_, ok := c.isSet[key]
diff --git a/pkg/innerring/config/fschain.go b/pkg/innerring/config/fschain.go
index 2e84a6a2f2..91f75192e1 100644
--- a/pkg/innerring/config/fschain.go
+++ b/pkg/innerring/config/fschain.go
@@ -8,9 +8,10 @@ import (
 
 // Chain configures settings of FS chain.
 type Chain struct {
-	BasicChain `mapstructure:",squash"`
-	Validators keys.PublicKeys `mapstructure:"validators"`
-	Consensus  Consensus       `mapstructure:"consensus"`
+	BasicChain        `mapstructure:",squash"`
+	Validators        keys.PublicKeys `mapstructure:"validators"`
+	Consensus         Consensus       `mapstructure:"consensus"`
+	DisableAutodeploy bool            `mapstructure:"disable_autodeploy"`
 }
 
 // Consensus configures Blockchain. All required fields must be set. Specified
diff --git a/pkg/innerring/innerring.go b/pkg/innerring/innerring.go
index 9f03147817..32057f2c5a 100644
--- a/pkg/innerring/innerring.go
+++ b/pkg/innerring/innerring.go
@@ -418,6 +418,15 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 
 	serveMetrics(server, cfg)
 
+	// TODO: remove deprecated 'fschain_autodeploy' config option in future release
+	if cfg.IsSet("fschain_autodeploy") {
+		log.Warn("configuration option 'fschain_autodeploy' is deprecated, use 'fschain.disable_autodeploy' with the opposite value instead")
+		if cfg.IsSet("fschain.disable_autodeploy") {
+			return nil, fmt.Errorf("'fschain_autodeploy' and 'fschain.disable_autodeploy' set simultaneously")
+		}
+		cfg.FSChain.DisableAutodeploy = !cfg.FSChainAutodeploy
+	}
+
 	var localWSClient *rpcclient.WSClient // set if isLocalConsensus only
 
 	// create FS chain client
@@ -472,7 +481,7 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		fsChainOpts[1] = client.WithLogger(log)
 		fsChainOpts[2] = client.WithSingleClient(localWSClient)
 
-		if !cfg.FSChainAutodeploy {
+		if cfg.FSChain.DisableAutodeploy {
 			fsChainOpts = append(fsChainOpts, client.WithAutoFSChainScope())
 		}
 
@@ -488,7 +497,7 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		// fallback to the pure RPC architecture
 
 		fsChainParams.key = server.key
-		fsChainParams.withAutoFSChainScope = !cfg.FSChainAutodeploy
+		fsChainParams.withAutoFSChainScope = cfg.FSChain.DisableAutodeploy
 
 		server.fsChainClient, err = server.createClient(ctx, fsChainParams, errChan)
 		if err != nil {
@@ -496,7 +505,7 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		}
 	}
 
-	if cfg.FSChainAutodeploy {
+	if !cfg.FSChain.DisableAutodeploy {
 		log.Info("auto-deployment configured, initializing FS chain...")
 
 		var fschain *fsChain
@@ -573,7 +582,15 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		return nil, err
 	}
 
-	server.withoutMainNet = cfg.WithoutMainnet
+	// TODO: remove deprecated 'without_mainnet' config option in future release
+	if cfg.IsSet("without_mainnet") {
+		log.Warn("configuration option 'without_mainnet' is deprecated, use 'mainnet.enabled' with the reverted value instead")
+		if cfg.IsSet("mainnet.enabled") {
+			return nil, fmt.Errorf("'without_mainnet' and 'mainnet.enabled' set simultaneously")
+		}
+		cfg.Mainnet.Enabled = !cfg.WithoutMainnet
+	}
+	server.withoutMainNet = !cfg.Mainnet.Enabled
 
 	if server.withoutMainNet {
 		// This works as long as event Listener starts listening loop once,
@@ -585,7 +602,7 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		mainnetChain := fsChainParams
 		mainnetChain.withAutoFSChainScope = false
 		mainnetChain.name = mainnetPrefix
-		mainnetChain.cfg = &cfg.Mainnet
+		mainnetChain.cfg = &cfg.Mainnet.BasicChain
 
 		mainnetChain.from, err = server.persistate.UInt32(persistateMainChainLastBlockKey)
 		if err != nil {
@@ -612,9 +629,18 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		zap.Bool("mainchain_enabled", !server.mainNotaryConfig.disabled),
 	)
 
+	// TODO: remove deprecated 'contracts' config option in future release
+	if cfg.IsSet("contracts") {
+		log.Warn("configuration option 'contracts' is deprecated, use 'mainnet.contracts' with the same values instead")
+		if cfg.IsSet("mainnet.contracts") {
+			return nil, fmt.Errorf("'contracts' and 'mainnet.contracts' set simultaneously")
+		}
+		cfg.Mainnet.Contracts = cfg.Contracts
+	}
+
 	// get all script hashes of contracts
 	server.contracts, err = initContracts(ctx, log,
-		&cfg.Contracts,
+		&cfg.Mainnet.Contracts,
 		server.fsChainClient,
 		server.withoutMainNet,
 		server.mainNotaryConfig.disabled,
@@ -672,8 +698,17 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 		return nil, err
 	}
 
+	// TODO: remove deprecated 'fee.main_chain' config option in future release
+	if cfg.IsSet("fee.main_chain") {
+		log.Warn("configuration option 'fee.main_chain' is deprecated, use 'mainnet.extra_fee' with the same value instead")
+		if cfg.IsSet("mainnet.extra_fee") {
+			return nil, fmt.Errorf("'fee.main_chain' and 'mainnet.extra_fee' set simultaneously")
+		}
+		cfg.Mainnet.ExtraFee = cfg.Fee.MainChain
+	}
+
 	neofsCli, err := neofsClient.NewFromMorph(server.mainnetClient, server.contracts.neofs,
-		fixedn.Fixed8(cfg.Fee.MainChain), neofsClient.TryNotary(), neofsClient.AsAlphabet())
+		fixedn.Fixed8(cfg.Mainnet.ExtraFee), neofsClient.TryNotary(), neofsClient.AsAlphabet())
 	if err != nil {
 		return nil, err
 	}
@@ -713,7 +748,16 @@ func New(ctx context.Context, log *zap.Logger, cfg *config.Config, errChan chan<
 
 	var alphaSync event.Handler
 
-	if server.withoutMainNet || cfg.Governance.Disable {
+	// TODO: remove deprecated 'governance.disable' config option in future release
+	if cfg.IsSet("governance.disable") {
+		log.Warn("configuration option 'governance.disable' is deprecated, use 'mainnet.disable_governance_sync' with the same value instead")
+		if cfg.IsSet("mainnet.disable_governance_sync") {
+			return nil, fmt.Errorf("'governance.disable' and 'mainnet.disable_governance_sync' set simultaneously")
+		}
+		cfg.Mainnet.DisableGovernanceSync = cfg.Governance.Disable
+	}
+
+	if server.withoutMainNet || cfg.Mainnet.DisableGovernanceSync {
 		alphaSync = func(event.Event) {
 			log.Debug("alphabet keys sync is disabled")
 		}