diff --git a/cmd/tailscale/cli/cli_test.go b/cmd/tailscale/cli/cli_test.go
index c1fe9b70a..c2e092aa5 100644
--- a/cmd/tailscale/cli/cli_test.go
+++ b/cmd/tailscale/cli/cli_test.go
@@ -786,7 +786,7 @@ func TestPrefFlagMapping(t *testing.T) {
 	prefHasFlag := map[string]bool{}
 	for _, pv := range prefsOfFlag {
 		for _, pref := range pv {
-			prefHasFlag[pref] = true
+			prefHasFlag[strings.Split(pref, ".")[0]] = true
 		}
 	}
 
diff --git a/cmd/tailscale/cli/set.go b/cmd/tailscale/cli/set.go
index b436b4a9a..ffa0d6e6f 100644
--- a/cmd/tailscale/cli/set.go
+++ b/cmd/tailscale/cli/set.go
@@ -167,7 +167,7 @@ func runSet(ctx context.Context, args []string) (retErr error) {
 			return err
 		}
 	}
-	if maskedPrefs.AutoUpdateSet {
+	if maskedPrefs.AutoUpdateSet.ApplySet {
 		// On macsys, tailscaled will set the Sparkle auto-update setting. It
 		// does not use clientupdate.
 		if version.IsMacSysExt() {
diff --git a/cmd/tailscale/cli/up.go b/cmd/tailscale/cli/up.go
index e418c0504..67d6a3483 100644
--- a/cmd/tailscale/cli/up.go
+++ b/cmd/tailscale/cli/up.go
@@ -718,8 +718,8 @@ func init() {
 	addPrefFlagMapping("ssh", "RunSSH")
 	addPrefFlagMapping("webclient", "RunWebClient")
 	addPrefFlagMapping("nickname", "ProfileName")
-	addPrefFlagMapping("update-check", "AutoUpdate")
-	addPrefFlagMapping("auto-update", "AutoUpdate")
+	addPrefFlagMapping("update-check", "AutoUpdate.Check")
+	addPrefFlagMapping("auto-update", "AutoUpdate.Apply")
 	addPrefFlagMapping("advertise-connector", "AppConnector")
 	addPrefFlagMapping("posture-checking", "PostureChecking")
 }
@@ -728,9 +728,14 @@ func addPrefFlagMapping(flagName string, prefNames ...string) {
 	prefsOfFlag[flagName] = prefNames
 	prefType := reflect.TypeOf(ipn.Prefs{})
 	for _, pref := range prefNames {
-		// Crash at runtime if there's a typo in the prefName.
-		if _, ok := prefType.FieldByName(pref); !ok {
-			panic(fmt.Sprintf("invalid ipn.Prefs field %q", pref))
+		t := prefType
+		for _, name := range strings.Split(pref, ".") {
+			// Crash at runtime if there's a typo in the prefName.
+			f, ok := t.FieldByName(name)
+			if !ok {
+				panic(fmt.Sprintf("invalid ipn.Prefs field %q", pref))
+			}
+			t = f.Type
 		}
 	}
 }
@@ -751,7 +756,11 @@ func updateMaskedPrefsFromUpOrSetFlag(mp *ipn.MaskedPrefs, flagName string) {
 	}
 	if prefs, ok := prefsOfFlag[flagName]; ok {
 		for _, pref := range prefs {
-			reflect.ValueOf(mp).Elem().FieldByName(pref + "Set").SetBool(true)
+			f := reflect.ValueOf(mp).Elem()
+			for _, name := range strings.Split(pref, ".") {
+				f = f.FieldByName(name + "Set")
+			}
+			f.SetBool(true)
 		}
 		return
 	}
diff --git a/ipn/conf.go b/ipn/conf.go
index d55146d58..f795e5205 100644
--- a/ipn/conf.go
+++ b/ipn/conf.go
@@ -124,7 +124,7 @@ func (c *ConfigVAlpha) ToPrefs() (MaskedPrefs, error) {
 	}
 	if c.AutoUpdate != nil {
 		mp.AutoUpdate = *c.AutoUpdate
-		mp.AutoUpdateSet = true
+		mp.AutoUpdateSet = AutoUpdatePrefsMask{ApplySet: true, CheckSet: true}
 	}
 	return mp, nil
 }
diff --git a/ipn/prefs.go b/ipn/prefs.go
index bb9b193fa..3cf0dd3f9 100644
--- a/ipn/prefs.go
+++ b/ipn/prefs.go
@@ -248,38 +248,55 @@ type AppConnectorPrefs struct {
 }
 
 // MaskedPrefs is a Prefs with an associated bitmask of which fields are set.
-// Make sure that the bool you add here maintains the same ordering of fields
-// as the Prefs struct, because the ApplyEdits() function below relies on this
-// ordering to be the same.
+//
+// Each FooSet field maps to a corresponding Foo field in Prefs. FooSet can be
+// a struct, in which case inner fields of FooSet map to inner fields of Foo in
+// Prefs (see AutoUpdateSet for example).
 type MaskedPrefs struct {
 	Prefs
 
-	ControlURLSet             bool `json:",omitempty"`
-	RouteAllSet               bool `json:",omitempty"`
-	AllowSingleHostsSet       bool `json:",omitempty"`
-	ExitNodeIDSet             bool `json:",omitempty"`
-	ExitNodeIPSet             bool `json:",omitempty"`
-	ExitNodeAllowLANAccessSet bool `json:",omitempty"`
-	CorpDNSSet                bool `json:",omitempty"`
-	RunSSHSet                 bool `json:",omitempty"`
-	RunWebClientSet           bool `json:",omitempty"`
-	WantRunningSet            bool `json:",omitempty"`
-	LoggedOutSet              bool `json:",omitempty"`
-	ShieldsUpSet              bool `json:",omitempty"`
-	AdvertiseTagsSet          bool `json:",omitempty"`
-	HostnameSet               bool `json:",omitempty"`
-	NotepadURLsSet            bool `json:",omitempty"`
-	ForceDaemonSet            bool `json:",omitempty"`
-	EggSet                    bool `json:",omitempty"`
-	AdvertiseRoutesSet        bool `json:",omitempty"`
-	NoSNATSet                 bool `json:",omitempty"`
-	NetfilterModeSet          bool `json:",omitempty"`
-	OperatorUserSet           bool `json:",omitempty"`
-	ProfileNameSet            bool `json:",omitempty"`
-	AutoUpdateSet             bool `json:",omitempty"`
-	AppConnectorSet           bool `json:",omitempty"`
-	PostureCheckingSet        bool `json:",omitempty"`
-	NetfilterKindSet          bool `json:",omitempty"`
+	ControlURLSet             bool                `json:",omitempty"`
+	RouteAllSet               bool                `json:",omitempty"`
+	AllowSingleHostsSet       bool                `json:",omitempty"`
+	ExitNodeIDSet             bool                `json:",omitempty"`
+	ExitNodeIPSet             bool                `json:",omitempty"`
+	ExitNodeAllowLANAccessSet bool                `json:",omitempty"`
+	CorpDNSSet                bool                `json:",omitempty"`
+	RunSSHSet                 bool                `json:",omitempty"`
+	RunWebClientSet           bool                `json:",omitempty"`
+	WantRunningSet            bool                `json:",omitempty"`
+	LoggedOutSet              bool                `json:",omitempty"`
+	ShieldsUpSet              bool                `json:",omitempty"`
+	AdvertiseTagsSet          bool                `json:",omitempty"`
+	HostnameSet               bool                `json:",omitempty"`
+	NotepadURLsSet            bool                `json:",omitempty"`
+	ForceDaemonSet            bool                `json:",omitempty"`
+	EggSet                    bool                `json:",omitempty"`
+	AdvertiseRoutesSet        bool                `json:",omitempty"`
+	NoSNATSet                 bool                `json:",omitempty"`
+	NetfilterModeSet          bool                `json:",omitempty"`
+	OperatorUserSet           bool                `json:",omitempty"`
+	ProfileNameSet            bool                `json:",omitempty"`
+	AutoUpdateSet             AutoUpdatePrefsMask `json:",omitempty"`
+	AppConnectorSet           bool                `json:",omitempty"`
+	PostureCheckingSet        bool                `json:",omitempty"`
+	NetfilterKindSet          bool                `json:",omitempty"`
+}
+
+type AutoUpdatePrefsMask struct {
+	CheckSet bool `json:",omitempty"`
+	ApplySet bool `json:",omitempty"`
+}
+
+func (m AutoUpdatePrefsMask) Pretty(au AutoUpdatePrefs) string {
+	var fields []string
+	if m.CheckSet {
+		fields = append(fields, fmt.Sprintf("Check=%v", au.Check))
+	}
+	if m.ApplySet {
+		fields = append(fields, fmt.Sprintf("Apply=%v", au.Apply))
+	}
+	return strings.Join(fields, " ")
 }
 
 // ApplyEdits mutates p, assigning fields from m.Prefs for each MaskedPrefs
@@ -291,15 +308,36 @@ func (p *Prefs) ApplyEdits(m *MaskedPrefs) {
 	pv := reflect.ValueOf(p).Elem()
 	mv := reflect.ValueOf(m).Elem()
 	mpv := reflect.ValueOf(&m.Prefs).Elem()
-	fields := mv.NumField()
-	for i := 1; i < fields; i++ {
-		if mv.Field(i).Bool() {
-			newFieldValue := mpv.Field(i - 1)
-			pv.Field(i - 1).Set(newFieldValue)
+	applyPrefsEdits(mpv, pv, maskFields(mv))
+}
+
+func applyPrefsEdits(src, dst reflect.Value, mask map[string]reflect.Value) {
+	for n, m := range mask {
+		switch m.Kind() {
+		case reflect.Bool:
+			if m.Bool() {
+				dst.FieldByName(n).Set(src.FieldByName(n))
+			}
+		case reflect.Struct:
+			applyPrefsEdits(src.FieldByName(n), dst.FieldByName(n), maskFields(m))
+		default:
+			panic(fmt.Sprintf("unsupported mask field kind %v", m.Kind()))
 		}
 	}
 }
 
+func maskFields(v reflect.Value) map[string]reflect.Value {
+	mask := make(map[string]reflect.Value)
+	for i := 0; i < v.NumField(); i++ {
+		f := v.Type().Field(i).Name
+		if !strings.HasSuffix(f, "Set") {
+			continue
+		}
+		mask[strings.TrimSuffix(f, "Set")] = v.Field(i)
+	}
+	return mask
+}
+
 // IsEmpty reports whether there are no masks set or if m is nil.
 func (m *MaskedPrefs) IsEmpty() bool {
 	if m == nil {
@@ -308,7 +346,7 @@ func (m *MaskedPrefs) IsEmpty() bool {
 	mv := reflect.ValueOf(m).Elem()
 	fields := mv.NumField()
 	for i := 1; i < fields; i++ {
-		if mv.Field(i).Bool() {
+		if !mv.Field(i).IsZero() {
 			return false
 		}
 	}
@@ -347,15 +385,30 @@ func (m *MaskedPrefs) Pretty() string {
 
 	for i := 1; i < mt.NumField(); i++ {
 		name := mt.Field(i).Name
-		if mv.Field(i).Bool() {
-			if !first {
-				sb.WriteString(" ")
+		mf := mv.Field(i)
+		switch mf.Kind() {
+		case reflect.Bool:
+			if mf.Bool() {
+				if !first {
+					sb.WriteString(" ")
+				}
+				first = false
+				f := mpv.Field(i - 1)
+				fmt.Fprintf(&sb, format(f),
+					strings.TrimSuffix(name, "Set"),
+					f.Interface())
+			}
+		case reflect.Struct:
+			if mf.IsZero() {
+				continue
+			}
+			mpf := mpv.Field(i - 1)
+			prettyFn := mf.MethodByName("Pretty")
+			if !prettyFn.IsValid() {
+				panic(fmt.Sprintf("MaskedPrefs field %q is missing the Pretty method", name))
 			}
-			first = false
-			f := mpv.Field(i - 1)
-			fmt.Fprintf(&sb, format(f),
-				strings.TrimSuffix(name, "Set"),
-				f.Interface())
+			res := prettyFn.Call([]reflect.Value{mpf})
+			fmt.Fprintf(&sb, "%s={%s}", strings.TrimSuffix(name, "Set"), res[0].String())
 		}
 	}
 	sb.WriteString("}")
diff --git a/ipn/prefs_test.go b/ipn/prefs_test.go
index f3987d2bf..1a09a94a9 100644
--- a/ipn/prefs_test.go
+++ b/ipn/prefs_test.go
@@ -761,6 +761,42 @@ func TestMaskedPrefsPretty(t *testing.T) {
 			},
 			want: `MaskedPrefs{ExitNodeIP=100.102.104.105}`,
 		},
+		{
+			m: &MaskedPrefs{
+				Prefs: Prefs{
+					AutoUpdate: AutoUpdatePrefs{Check: true, Apply: false},
+				},
+				AutoUpdateSet: AutoUpdatePrefsMask{CheckSet: true, ApplySet: false},
+			},
+			want: `MaskedPrefs{AutoUpdate={Check=true}}`,
+		},
+		{
+			m: &MaskedPrefs{
+				Prefs: Prefs{
+					AutoUpdate: AutoUpdatePrefs{Check: true, Apply: true},
+				},
+				AutoUpdateSet: AutoUpdatePrefsMask{CheckSet: true, ApplySet: true},
+			},
+			want: `MaskedPrefs{AutoUpdate={Check=true Apply=true}}`,
+		},
+		{
+			m: &MaskedPrefs{
+				Prefs: Prefs{
+					AutoUpdate: AutoUpdatePrefs{Check: true, Apply: false},
+				},
+				AutoUpdateSet: AutoUpdatePrefsMask{CheckSet: false, ApplySet: true},
+			},
+			want: `MaskedPrefs{AutoUpdate={Apply=false}}`,
+		},
+		{
+			m: &MaskedPrefs{
+				Prefs: Prefs{
+					AutoUpdate: AutoUpdatePrefs{Check: true, Apply: true},
+				},
+				AutoUpdateSet: AutoUpdatePrefsMask{CheckSet: false, ApplySet: false},
+			},
+			want: `MaskedPrefs{}`,
+		},
 	}
 	for i, tt := range tests {
 		got := tt.m.Pretty()