diff --git a/internal/doctor/config_check.go b/internal/doctor/config_check.go
index 76ff9b3ee3..51d591f126 100644
--- a/internal/doctor/config_check.go
+++ b/internal/doctor/config_check.go
@@ -10,6 +10,7 @@ import (
 	"sort"
 	"strings"
 
+	"github.com/steveyegge/gastown/internal/beads"
 	"github.com/steveyegge/gastown/internal/constants"
 )
 
@@ -605,8 +606,8 @@ func containsFlag(s, flag string) bool {
 // CustomTypesCheck verifies Gas Town custom types are registered with beads.
 type CustomTypesCheck struct {
 	FixableCheck
-	missingTypes []string // Cached during Run for use in Fix
-	townRoot     string   // Cached during Run for use in Fix
+	missingTypes   []string // Cached during Run for use in Fix
+	targetBeadsDir string   // Cached during Run for use in Fix
 }
 
 // NewCustomTypesCheck creates a new custom types check.
@@ -633,9 +634,8 @@ func (c *CustomTypesCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 	}
 
-	// Check if .beads directory exists at town level
-	townBeadsDir := filepath.Join(ctx.TownRoot, ".beads")
-	if _, err := os.Stat(townBeadsDir); os.IsNotExist(err) {
+	beadsDir := doctorConfigBeadsDir(ctx)
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
 		return &CheckResult{
 			Name:    c.Name(),
 			Status:  StatusOK,
@@ -646,11 +646,12 @@ func (c *CustomTypesCheck) Run(ctx *CheckContext) *CheckResult {
 	// Get current custom types configuration
 	// Use Output() not CombinedOutput() to avoid capturing bd's stderr messages
 	cmd := exec.Command("bd", "config", "get", "types.custom")
-	cmd.Dir = ctx.TownRoot
+	cmd.Dir = beadsDir
+	cmd.Env = doctorConfigEnv(beadsDir)
 	output, err := cmd.Output()
 	if err != nil {
 		// If config key doesn't exist, types are not configured
-		c.townRoot = ctx.TownRoot
+		c.targetBeadsDir = beadsDir
 		c.missingTypes = constants.BeadsCustomTypesList()
 		return &CheckResult{
 			Name:    c.Name(),
@@ -690,7 +691,7 @@ func (c *CustomTypesCheck) Run(ctx *CheckContext) *CheckResult {
 	}
 
 	// Cache for Fix
-	c.townRoot = ctx.TownRoot
+	c.targetBeadsDir = beadsDir
 	c.missingTypes = missing
 
 	return &CheckResult{
@@ -720,8 +721,33 @@ func parseConfigOutput(output []byte) string {
 
 // Fix registers the missing custom types.
 func (c *CustomTypesCheck) Fix(ctx *CheckContext) error {
-	cmd := exec.Command("bd", "config", "set", "types.custom", constants.BeadsCustomTypes)
-	cmd.Dir = c.townRoot
+	getCmd := exec.Command("bd", "config", "get", "types.custom")
+	getCmd.Dir = c.targetBeadsDir
+	getCmd.Env = doctorConfigEnv(c.targetBeadsDir)
+	existingOutput, _ := getCmd.Output()
+
+	typeSet := make(map[string]bool)
+	if existing := parseConfigOutput(existingOutput); existing != "" {
+		for _, typ := range strings.Split(existing, ",") {
+			typ = strings.TrimSpace(typ)
+			if typ != "" {
+				typeSet[typ] = true
+			}
+		}
+	}
+	for _, typ := range constants.BeadsCustomTypesList() {
+		typeSet[typ] = true
+	}
+
+	var merged []string
+	for typ := range typeSet {
+		merged = append(merged, typ)
+	}
+	sort.Strings(merged)
+
+	cmd := exec.Command("bd", "config", "set", "types.custom", strings.Join(merged, ","))
+	cmd.Dir = c.targetBeadsDir
+	cmd.Env = doctorConfigEnv(c.targetBeadsDir)
 	output, err := cmd.CombinedOutput()
 	if err != nil {
 		return fmt.Errorf("bd config set types.custom: %s", strings.TrimSpace(string(output)))
@@ -733,7 +759,7 @@ func (c *CustomTypesCheck) Fix(ctx *CheckContext) error {
 type CustomStatusesCheck struct {
 	FixableCheck
 	missingStatuses []string // Cached during Run for use in Fix
-	townRoot        string   // Cached during Run for use in Fix
+	targetBeadsDir  string   // Cached during Run for use in Fix
 }
 
 // NewCustomStatusesCheck creates a new custom statuses check.
@@ -759,8 +785,8 @@ func (c *CustomStatusesCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 	}
 
-	townBeadsDir := filepath.Join(ctx.TownRoot, ".beads")
-	if _, err := os.Stat(townBeadsDir); os.IsNotExist(err) {
+	beadsDir := doctorConfigBeadsDir(ctx)
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
 		return &CheckResult{
 			Name:    c.Name(),
 			Status:  StatusOK,
@@ -770,10 +796,11 @@ func (c *CustomStatusesCheck) Run(ctx *CheckContext) *CheckResult {
 
 	// Get current custom statuses configuration
 	cmd := exec.Command("bd", "config", "get", "status.custom")
-	cmd.Dir = ctx.TownRoot
+	cmd.Dir = beadsDir
+	cmd.Env = doctorConfigEnv(beadsDir)
 	output, err := cmd.Output()
 	if err != nil {
-		c.townRoot = ctx.TownRoot
+		c.targetBeadsDir = beadsDir
 		c.missingStatuses = constants.BeadsCustomStatusesList()
 		return &CheckResult{
 			Name:    c.Name(),
@@ -810,7 +837,7 @@ func (c *CustomStatusesCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 	}
 
-	c.townRoot = ctx.TownRoot
+	c.targetBeadsDir = beadsDir
 	c.missingStatuses = missing
 
 	return &CheckResult{
@@ -830,7 +857,8 @@ func (c *CustomStatusesCheck) Run(ctx *CheckContext) *CheckResult {
 func (c *CustomStatusesCheck) Fix(ctx *CheckContext) error {
 	// Read existing statuses
 	getCmd := exec.Command("bd", "config", "get", "status.custom")
-	getCmd.Dir = c.townRoot
+	getCmd.Dir = c.targetBeadsDir
+	getCmd.Env = doctorConfigEnv(c.targetBeadsDir)
 	existingOutput, _ := getCmd.Output()
 
 	// Build merged set
@@ -854,10 +882,45 @@ func (c *CustomStatusesCheck) Fix(ctx *CheckContext) error {
 	sort.Strings(merged)
 
 	cmd := exec.Command("bd", "config", "set", "status.custom", strings.Join(merged, ","))
-	cmd.Dir = c.townRoot
+	cmd.Dir = c.targetBeadsDir
+	cmd.Env = doctorConfigEnv(c.targetBeadsDir)
 	output, err := cmd.CombinedOutput()
 	if err != nil {
 		return fmt.Errorf("bd config set status.custom: %s", strings.TrimSpace(string(output)))
 	}
 	return nil
 }
+
+func doctorConfigBeadsDir(ctx *CheckContext) string {
+	workDir := ctx.TownRoot
+	if ctx.RigName != "" {
+		workDir = ctx.RigPath()
+	}
+	return beads.ResolveBeadsDir(workDir)
+}
+
+func doctorConfigEnv(beadsDir string) []string {
+	env := stripEnvPrefixes(os.Environ(), "BEADS_DIR=", "BEADS_DB=", "BEADS_DOLT_SERVER_DATABASE=")
+	env = append(env, "BEADS_DIR="+beadsDir)
+	if dbEnv := beads.DatabaseEnv(beadsDir); dbEnv != "" {
+		env = append(env, dbEnv)
+	}
+	return env
+}
+
+func stripEnvPrefixes(env []string, prefixes ...string) []string {
+	filtered := make([]string, 0, len(env))
+	for _, entry := range env {
+		skip := false
+		for _, prefix := range prefixes {
+			if strings.HasPrefix(entry, prefix) {
+				skip = true
+				break
+			}
+		}
+		if !skip {
+			filtered = append(filtered, entry)
+		}
+	}
+	return filtered
+}
diff --git a/internal/doctor/config_check_test.go b/internal/doctor/config_check_test.go
index d5267d4418..c13141a712 100644
--- a/internal/doctor/config_check_test.go
+++ b/internal/doctor/config_check_test.go
@@ -1,6 +1,7 @@
 package doctor
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -9,6 +10,94 @@ import (
 	"github.com/steveyegge/gastown/internal/constants"
 )
 
+func installFakeBdForConfigChecks(t *testing.T, townRoot string) {
+	t.Helper()
+
+	binDir := filepath.Join(townRoot, "bin")
+	if err := os.MkdirAll(binDir, 0755); err != nil {
+		t.Fatalf("mkdir fake bin: %v", err)
+	}
+
+	script := `#!/bin/sh
+set -eu
+
+target="${BEADS_DIR:-$PWD}"
+if [ -d "$target/.beads" ]; then
+  target="$target/.beads"
+fi
+
+case "$1:$2:$3" in
+  config:get:types.custom)
+    if [ -f "$target/types.custom" ]; then
+      cat "$target/types.custom"
+    else
+      exit 1
+    fi
+    ;;
+  config:set:types.custom)
+    printf '%s\n' "$4" > "$target/types.custom"
+    ;;
+  config:get:status.custom)
+    if [ -f "$target/status.custom" ]; then
+      cat "$target/status.custom"
+    else
+      exit 1
+    fi
+    ;;
+  config:set:status.custom)
+    printf '%s\n' "$4" > "$target/status.custom"
+    ;;
+  *)
+    echo "unexpected bd invocation: $*" >&2
+    exit 1
+    ;;
+esac
+`
+
+	bdPath := filepath.Join(binDir, "bd")
+	if err := os.WriteFile(bdPath, []byte(script), 0755); err != nil {
+		t.Fatalf("write fake bd: %v", err)
+	}
+
+	oldPath := os.Getenv("PATH")
+	if err := os.Setenv("PATH", fmt.Sprintf("%s:%s", binDir, oldPath)); err != nil {
+		t.Fatalf("set PATH: %v", err)
+	}
+	t.Cleanup(func() {
+		_ = os.Setenv("PATH", oldPath)
+	})
+	for _, key := range []string{"BEADS_DIR", "BEADS_DB", "BEADS_DOLT_SERVER_DATABASE"} {
+		oldVal, hadVal := os.LookupEnv(key)
+		_ = os.Unsetenv(key)
+		t.Cleanup(func() {
+			if hadVal {
+				_ = os.Setenv(key, oldVal)
+			} else {
+				_ = os.Unsetenv(key)
+			}
+		})
+	}
+}
+
+func writeConfigCheckFile(t *testing.T, beadsDir, name, value string) {
+	t.Helper()
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("mkdir beads dir: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, name), []byte(value+"\n"), 0644); err != nil {
+		t.Fatalf("write %s: %v", name, err)
+	}
+}
+
+func readConfigCheckFile(t *testing.T, beadsDir, name string) string {
+	t.Helper()
+	data, err := os.ReadFile(filepath.Join(beadsDir, name))
+	if err != nil {
+		t.Fatalf("read %s: %v", name, err)
+	}
+	return strings.TrimSpace(string(data))
+}
+
 func TestSessionHookCheck_UsesSessionStartScript(t *testing.T) {
 	check := NewSessionHookCheck()
 
@@ -482,3 +571,122 @@ func TestCustomStatusesCheck_ParsesOutputWithNotePrefix(t *testing.T) {
 		t.Errorf("After parsing, missing statuses: %v", missing)
 	}
 }
+
+func TestCustomTypesCheck_UsesRigScopedBeadsDir(t *testing.T) {
+	townRoot := t.TempDir()
+	rigDir := filepath.Join(townRoot, "gastown")
+	townBeadsDir := filepath.Join(townRoot, ".beads")
+	rigBeadsDir := filepath.Join(rigDir, ".beads")
+
+	writeConfigCheckFile(t, townBeadsDir, "types.custom", constants.BeadsCustomTypes)
+	writeConfigCheckFile(t, rigBeadsDir, "types.custom", "agent,role")
+	installFakeBdForConfigChecks(t, townRoot)
+
+	check := NewCustomTypesCheck()
+	ctx := &CheckContext{TownRoot: townRoot, RigName: "gastown"}
+
+	result := check.Run(ctx)
+	if result.Status != StatusWarning {
+		t.Fatalf("expected StatusWarning, got %v (%v)", result.Status, result.Details)
+	}
+	if check.targetBeadsDir != rigBeadsDir {
+		t.Fatalf("Run cached %q, want %q", check.targetBeadsDir, rigBeadsDir)
+	}
+
+	if err := check.Fix(ctx); err != nil {
+		t.Fatalf("Fix failed: %v", err)
+	}
+
+	gotTypes := strings.Split(readConfigCheckFile(t, rigBeadsDir, "types.custom"), ",")
+	wantTypes := make(map[string]struct{})
+	for _, item := range constants.BeadsCustomTypesList() {
+		wantTypes[item] = struct{}{}
+	}
+	for _, item := range gotTypes {
+		delete(wantTypes, item)
+	}
+	if len(wantTypes) != 0 {
+		t.Fatalf("rig types.custom missing expected entries after fix: %v (got %q)", wantTypes, strings.Join(gotTypes, ","))
+	}
+	if got := readConfigCheckFile(t, townBeadsDir, "types.custom"); got != constants.BeadsCustomTypes {
+		t.Fatalf("town types.custom changed unexpectedly: %q", got)
+	}
+
+	result = check.Run(ctx)
+	if result.Status != StatusOK {
+		t.Fatalf("expected StatusOK after fix, got %v (%v)", result.Status, result.Details)
+	}
+}
+
+func TestCustomTypesCheck_FixPreservesExistingRigTypes(t *testing.T) {
+	townRoot := t.TempDir()
+	rigDir := filepath.Join(townRoot, "gastown")
+	townBeadsDir := filepath.Join(townRoot, ".beads")
+	rigBeadsDir := filepath.Join(rigDir, ".beads")
+
+	writeConfigCheckFile(t, townBeadsDir, "types.custom", constants.BeadsCustomTypes)
+	writeConfigCheckFile(t, rigBeadsDir, "types.custom", "agent,role,external")
+	installFakeBdForConfigChecks(t, townRoot)
+
+	check := NewCustomTypesCheck()
+	ctx := &CheckContext{TownRoot: townRoot, RigName: "gastown"}
+
+	result := check.Run(ctx)
+	if result.Status != StatusWarning {
+		t.Fatalf("expected StatusWarning, got %v (%v)", result.Status, result.Details)
+	}
+
+	if err := check.Fix(ctx); err != nil {
+		t.Fatalf("Fix failed: %v", err)
+	}
+
+	got := strings.Split(readConfigCheckFile(t, rigBeadsDir, "types.custom"), ",")
+	wantSet := make(map[string]struct{})
+	for _, item := range append(constants.BeadsCustomTypesList(), "external") {
+		wantSet[item] = struct{}{}
+	}
+	for _, item := range got {
+		delete(wantSet, item)
+	}
+	if len(wantSet) != 0 {
+		t.Fatalf("rig types.custom missing expected entries after fix: %v (got %q)", wantSet, strings.Join(got, ","))
+	}
+}
+
+func TestCustomStatusesCheck_UsesRigScopedBeadsDir(t *testing.T) {
+	townRoot := t.TempDir()
+	rigDir := filepath.Join(townRoot, "gastown")
+	townBeadsDir := filepath.Join(townRoot, ".beads")
+	rigBeadsDir := filepath.Join(rigDir, ".beads")
+
+	writeConfigCheckFile(t, townBeadsDir, "status.custom", constants.BeadsCustomStatuses)
+	writeConfigCheckFile(t, rigBeadsDir, "status.custom", "queued")
+	installFakeBdForConfigChecks(t, townRoot)
+
+	check := NewCustomStatusesCheck()
+	ctx := &CheckContext{TownRoot: townRoot, RigName: "gastown"}
+
+	result := check.Run(ctx)
+	if result.Status != StatusWarning {
+		t.Fatalf("expected StatusWarning, got %v (%v)", result.Status, result.Details)
+	}
+	if check.targetBeadsDir != rigBeadsDir {
+		t.Fatalf("Run cached %q, want %q", check.targetBeadsDir, rigBeadsDir)
+	}
+
+	if err := check.Fix(ctx); err != nil {
+		t.Fatalf("Fix failed: %v", err)
+	}
+
+	if got := readConfigCheckFile(t, rigBeadsDir, "status.custom"); got != "queued,"+constants.BeadsCustomStatuses {
+		t.Fatalf("rig status.custom = %q", got)
+	}
+	if got := readConfigCheckFile(t, townBeadsDir, "status.custom"); got != constants.BeadsCustomStatuses {
+		t.Fatalf("town status.custom changed unexpectedly: %q", got)
+	}
+
+	result = check.Run(ctx)
+	if result.Status != StatusOK {
+		t.Fatalf("expected StatusOK after fix, got %v (%v)", result.Status, result.Details)
+	}
+}