diff --git a/client/internal/routemanager/manager.go b/client/internal/routemanager/manager.go
index 04513bbe4..d590dba0d 100644
--- a/client/internal/routemanager/manager.go
+++ b/client/internal/routemanager/manager.go
@@ -106,7 +106,7 @@ type DefaultManager struct {
 func NewManager(config ManagerConfig) *DefaultManager {
 	mCTX, cancel := context.WithCancel(config.Context)
 	notifier := notifier.NewNotifier()
-	sysOps := systemops.NewSysOps(config.WGInterface, notifier)
+	sysOps := systemops.New(config.WGInterface, notifier)
 
 	if runtime.GOOS == "windows" && config.WGInterface != nil {
 		nbnet.SetVPNInterfaceName(config.WGInterface.Name())
diff --git a/client/internal/routemanager/systemops/flush_nonbsd.go b/client/internal/routemanager/systemops/flush_nonbsd.go
new file mode 100644
index 000000000..f1c45d6cf
--- /dev/null
+++ b/client/internal/routemanager/systemops/flush_nonbsd.go
@@ -0,0 +1,8 @@
+//go:build !((darwin && !ios) || dragonfly || freebsd || netbsd || openbsd)
+
+package systemops
+
+// FlushMarkedRoutes is a no-op on non-BSD platforms.
+func (r *SysOps) FlushMarkedRoutes() error {
+	return nil
+}
diff --git a/client/internal/routemanager/systemops/state.go b/client/internal/routemanager/systemops/state.go
index 8e158711e..e0d045b07 100644
--- a/client/internal/routemanager/systemops/state.go
+++ b/client/internal/routemanager/systemops/state.go
@@ -13,11 +13,11 @@ func (s *ShutdownState) Name() string {
 }
 
 func (s *ShutdownState) Cleanup() error {
-	sysops := NewSysOps(nil, nil)
-	sysops.refCounter = refcounter.New[netip.Prefix, struct{}, Nexthop](nil, sysops.removeFromRouteTable)
-	sysops.refCounter.LoadData((*ExclusionCounter)(s))
+	sysOps := New(nil, nil)
+	sysOps.refCounter = refcounter.New[netip.Prefix, struct{}, Nexthop](nil, sysOps.removeFromRouteTable)
+	sysOps.refCounter.LoadData((*ExclusionCounter)(s))
 
-	return sysops.refCounter.Flush()
+	return sysOps.refCounter.Flush()
 }
 
 func (s *ShutdownState) MarshalJSON() ([]byte, error) {
diff --git a/client/internal/routemanager/systemops/systemops.go b/client/internal/routemanager/systemops/systemops.go
index 8da138117..c0ca21d22 100644
--- a/client/internal/routemanager/systemops/systemops.go
+++ b/client/internal/routemanager/systemops/systemops.go
@@ -83,7 +83,7 @@ type SysOps struct {
 	localSubnetsCacheTime time.Time
 }
 
-func NewSysOps(wgInterface wgIface, notifier *notifier.Notifier) *SysOps {
+func New(wgInterface wgIface, notifier *notifier.Notifier) *SysOps {
 	return &SysOps{
 		wgInterface: wgInterface,
 		notifier:    notifier,
diff --git a/client/internal/routemanager/systemops/systemops_bsd_test.go b/client/internal/routemanager/systemops/systemops_bsd_test.go
index 0d892c162..ec4fc406e 100644
--- a/client/internal/routemanager/systemops/systemops_bsd_test.go
+++ b/client/internal/routemanager/systemops/systemops_bsd_test.go
@@ -42,7 +42,7 @@ func TestConcurrentRoutes(t *testing.T) {
 	_, intf = setupDummyInterface(t)
 	nexthop = Nexthop{netip.Addr{}, intf}
 
-	r := NewSysOps(nil, nil)
+	r := New(nil, nil)
 
 	var wg sync.WaitGroup
 	for i := 0; i < 1024; i++ {
@@ -146,7 +146,7 @@ func createAndSetupDummyInterface(t *testing.T, intf string, ipAddressCIDR strin
 
 	nexthop := Nexthop{netip.Addr{}, netIntf}
 
-	r := NewSysOps(nil, nil)
+	r := New(nil, nil)
 	err = r.addToRouteTable(prefix, nexthop)
 	require.NoError(t, err, "Failed to add route to table")
 
diff --git a/client/internal/routemanager/systemops/systemops_generic_test.go b/client/internal/routemanager/systemops/systemops_generic_test.go
index 32ea38a7a..d9b109beb 100644
--- a/client/internal/routemanager/systemops/systemops_generic_test.go
+++ b/client/internal/routemanager/systemops/systemops_generic_test.go
@@ -143,7 +143,7 @@ func TestAddVPNRoute(t *testing.T) {
 
 			wgInterface := createWGInterface(t, fmt.Sprintf("utun53%d", n), "100.65.75.2/24", 33100+n)
 
-			r := NewSysOps(wgInterface, nil)
+			r := New(wgInterface, nil)
 			advancedRouting := nbnet.AdvancedRouting()
 			err := r.SetupRouting(nil, nil, advancedRouting)
 			require.NoError(t, err)
@@ -342,7 +342,7 @@ func TestAddRouteToNonVPNIntf(t *testing.T) {
 
 			wgInterface := createWGInterface(t, fmt.Sprintf("utun54%d", n), "100.65.75.2/24", 33200+n)
 
-			r := NewSysOps(wgInterface, nil)
+			r := New(wgInterface, nil)
 			advancedRouting := nbnet.AdvancedRouting()
 			err := r.SetupRouting(nil, nil, advancedRouting)
 			require.NoError(t, err)
@@ -486,7 +486,7 @@ func setupTestEnv(t *testing.T) {
 		assert.NoError(t, wgInterface.Close())
 	})
 
-	r := NewSysOps(wgInterface, nil)
+	r := New(wgInterface, nil)
 	advancedRouting := nbnet.AdvancedRouting()
 	err := r.SetupRouting(nil, nil, advancedRouting)
 	require.NoError(t, err, "setupRouting should not return err")
diff --git a/client/internal/routemanager/systemops/systemops_unix.go b/client/internal/routemanager/systemops/systemops_unix.go
index d43c2d5bf..7089178fb 100644
--- a/client/internal/routemanager/systemops/systemops_unix.go
+++ b/client/internal/routemanager/systemops/systemops_unix.go
@@ -7,19 +7,39 @@ import (
 	"fmt"
 	"net"
 	"net/netip"
+	"os"
 	"strconv"
 	"syscall"
 	"time"
 	"unsafe"
 
 	"github.com/cenkalti/backoff/v4"
+	"github.com/hashicorp/go-multierror"
 	log "github.com/sirupsen/logrus"
 	"golang.org/x/net/route"
 	"golang.org/x/sys/unix"
 
+	nberrors "github.com/netbirdio/netbird/client/errors"
 	"github.com/netbirdio/netbird/client/internal/statemanager"
 )
 
+const (
+	envRouteProtoFlag = "NB_ROUTE_PROTO_FLAG"
+)
+
+var routeProtoFlag int
+
+func init() {
+	switch os.Getenv(envRouteProtoFlag) {
+	case "2":
+		routeProtoFlag = unix.RTF_PROTO2
+	case "3":
+		routeProtoFlag = unix.RTF_PROTO3
+	default:
+		routeProtoFlag = unix.RTF_PROTO1
+	}
+}
+
 func (r *SysOps) SetupRouting(initAddresses []net.IP, stateManager *statemanager.Manager, advancedRouting bool) error {
 	return r.setupRefCounter(initAddresses, stateManager)
 }
@@ -28,6 +48,62 @@ func (r *SysOps) CleanupRouting(stateManager *statemanager.Manager, advancedRout
 	return r.cleanupRefCounter(stateManager)
 }
 
+// FlushMarkedRoutes removes single IP exclusion routes marked with the configured RTF_PROTO flag.
+func (r *SysOps) FlushMarkedRoutes() error {
+	rib, err := retryFetchRIB()
+	if err != nil {
+		return fmt.Errorf("fetch routing table: %w", err)
+	}
+
+	msgs, err := route.ParseRIB(route.RIBTypeRoute, rib)
+	if err != nil {
+		return fmt.Errorf("parse routing table: %w", err)
+	}
+
+	var merr *multierror.Error
+	flushedCount := 0
+
+	for _, msg := range msgs {
+		rtMsg, ok := msg.(*route.RouteMessage)
+		if !ok {
+			continue
+		}
+
+		if rtMsg.Flags&routeProtoFlag == 0 {
+			continue
+		}
+
+		routeInfo, err := MsgToRoute(rtMsg)
+		if err != nil {
+			log.Debugf("Skipping route flush: %v", err)
+			continue
+		}
+
+		if !routeInfo.Dst.IsValid() || !routeInfo.Dst.IsSingleIP() {
+			continue
+		}
+
+		nexthop := Nexthop{
+			IP:   routeInfo.Gw,
+			Intf: routeInfo.Interface,
+		}
+
+		if err := r.removeFromRouteTable(routeInfo.Dst, nexthop); err != nil {
+			merr = multierror.Append(merr, fmt.Errorf("remove route %s: %w", routeInfo.Dst, err))
+			continue
+		}
+
+		flushedCount++
+		log.Debugf("Flushed marked route: %s", routeInfo.Dst)
+	}
+
+	if flushedCount > 0 {
+		log.Infof("Flushed %d residual NetBird routes from previous session", flushedCount)
+	}
+
+	return nberrors.FormatErrorOrNil(merr)
+}
+
 func (r *SysOps) addToRouteTable(prefix netip.Prefix, nexthop Nexthop) error {
 	return r.routeSocket(unix.RTM_ADD, prefix, nexthop)
 }
@@ -105,7 +181,7 @@ func (r *SysOps) routeOp(action int, prefix netip.Prefix, nexthop Nexthop) func(
 func (r *SysOps) buildRouteMessage(action int, prefix netip.Prefix, nexthop Nexthop) (msg *route.RouteMessage, err error) {
 	msg = &route.RouteMessage{
 		Type:    action,
-		Flags:   unix.RTF_UP,
+		Flags:   unix.RTF_UP | routeProtoFlag,
 		Version: unix.RTM_VERSION,
 		Seq:     r.getSeq(),
 	}
diff --git a/client/internal/statemanager/manager.go b/client/internal/statemanager/manager.go
index 29f962ad2..2c9e46290 100644
--- a/client/internal/statemanager/manager.go
+++ b/client/internal/statemanager/manager.go
@@ -295,7 +295,7 @@ func (m *Manager) loadStateFile(deleteCorrupt bool) (map[string]json.RawMessage,
 	data, err := os.ReadFile(m.filePath)
 	if err != nil {
 		if errors.Is(err, fs.ErrNotExist) {
-			log.Debug("state file does not exist")
+			log.Debugf("state file %s does not exist", m.filePath)
 			return nil, nil // nolint:nilnil
 		}
 		return nil, fmt.Errorf("read state file: %w", err)
diff --git a/client/server/state.go b/client/server/state.go
index 107f55154..1cf85cd37 100644
--- a/client/server/state.go
+++ b/client/server/state.go
@@ -10,7 +10,9 @@ import (
 
 	nberrors "github.com/netbirdio/netbird/client/errors"
 	"github.com/netbirdio/netbird/client/internal"
+	"github.com/netbirdio/netbird/client/internal/routemanager/systemops"
 	"github.com/netbirdio/netbird/client/internal/statemanager"
+	nbnet "github.com/netbirdio/netbird/client/net"
 	"github.com/netbirdio/netbird/client/proto"
 )
 
@@ -135,5 +137,12 @@ func restoreResidualState(ctx context.Context, statePath string) error {
 		merr = multierror.Append(merr, fmt.Errorf("persist state: %w", err))
 	}
 
+	// clean up any remaining routes independently of the state file
+	if !nbnet.AdvancedRouting() {
+		if err := systemops.New(nil, nil).FlushMarkedRoutes(); err != nil {
+			merr = multierror.Append(merr, fmt.Errorf("flush marked routes: %w", err))
+		}
+	}
+
 	return nberrors.FormatErrorOrNil(merr)
 }