diff --git a/internal/config/yaml_config.go b/internal/config/yaml_config.go
index db659c98..cda4f695 100644
--- a/internal/config/yaml_config.go
+++ b/internal/config/yaml_config.go
@@ -74,14 +74,34 @@ func IsYamlOnlyKey(key string) bool {
 	return false
 }
 
+// keyAliases maps alternative key names to their canonical yaml form.
+// This ensures consistency when users use different formats (dot vs hyphen).
+var keyAliases = map[string]string{
+	"sync.branch": "sync-branch",
+}
+
+// normalizeYamlKey converts a key to its canonical yaml format.
+// Some keys have aliases (e.g., sync.branch -> sync-branch) to handle
+// different input formats consistently.
+func normalizeYamlKey(key string) string {
+	if canonical, ok := keyAliases[key]; ok {
+		return canonical
+	}
+	return key
+}
+
 // SetYamlConfig sets a configuration value in the project's config.yaml file.
 // It handles both adding new keys and updating existing (possibly commented) keys.
+// Keys are normalized to their canonical yaml format (e.g., sync.branch -> sync-branch).
 func SetYamlConfig(key, value string) error {
 	configPath, err := findProjectConfigYaml()
 	if err != nil {
 		return err
 	}
 
+	// Normalize key to canonical yaml format
+	normalizedKey := normalizeYamlKey(key)
+
 	// Read existing config
 	content, err := os.ReadFile(configPath) //nolint:gosec // configPath is from findProjectConfigYaml
 	if err != nil {
@@ -89,7 +109,7 @@ func SetYamlConfig(key, value string) error {
 	}
 
 	// Update or add the key
-	newContent, err := updateYamlKey(string(content), key, value)
+	newContent, err := updateYamlKey(string(content), normalizedKey, value)
 	if err != nil {
 		return err
 	}
@@ -194,12 +214,8 @@ func formatYamlValue(value string) string {
 		return value
 	}
 
-	// String values that need quoting
-	if needsQuoting(value) {
-		return fmt.Sprintf("%q", value)
-	}
-
-	return value
+	// For all other string-like values, quote to preserve YAML string semantics
+	return fmt.Sprintf("%q", value)
 }
 
 func isNumeric(s string) bool {
diff --git a/internal/config/yaml_config_test.go b/internal/config/yaml_config_test.go
index 6fefe8f3..9f09b6aa 100644
--- a/internal/config/yaml_config_test.go
+++ b/internal/config/yaml_config_test.go
@@ -92,7 +92,7 @@ func TestUpdateYamlKey(t *testing.T) {
 			content:  "# actor: \"\"\nother: value",
 			key:      "actor",
 			value:    "steve",
-			expected: "actor: steve\nother: value",
+			expected: "actor: \"steve\"\nother: value",
 		},
 		{
 			name:     "handle duration value",
@@ -136,8 +136,8 @@ func TestFormatYamlValue(t *testing.T) {
 		{"3.14", "3.14"},
 		{"30s", "30s"},
 		{"5m", "5m"},
-		{"simple", "simple"},
-		{"has space", "has space"},
+		{"simple", "\"simple\""},
+		{"has space", "\"has space\""},
 		{"has:colon", "\"has:colon\""},
 		{"has#hash", "\"has#hash\""},
 		{" leading", "\" leading\""},
@@ -153,6 +153,77 @@ func TestFormatYamlValue(t *testing.T) {
 	}
 }
 
+func TestNormalizeYamlKey(t *testing.T) {
+	tests := []struct {
+		input    string
+		expected string
+	}{
+		{"sync.branch", "sync-branch"},  // alias should be normalized
+		{"sync-branch", "sync-branch"},  // already canonical
+		{"no-db", "no-db"},              // no alias, unchanged
+		{"json", "json"},                // no alias, unchanged
+		{"routing.mode", "routing.mode"}, // no alias for this one
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.input, func(t *testing.T) {
+			got := normalizeYamlKey(tt.input)
+			if got != tt.expected {
+				t.Errorf("normalizeYamlKey(%q) = %q, want %q", tt.input, got, tt.expected)
+			}
+		})
+	}
+}
+
+func TestSetYamlConfig_KeyNormalization(t *testing.T) {
+	// Create a temp directory with .beads/config.yaml
+	tmpDir, err := os.MkdirTemp("", "beads-yaml-key-norm-*")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create .beads dir: %v", err)
+	}
+
+	configPath := filepath.Join(beadsDir, "config.yaml")
+	initialConfig := `# Beads Config
+sync-branch: old-value
+`
+	if err := os.WriteFile(configPath, []byte(initialConfig), 0644); err != nil {
+		t.Fatalf("Failed to write config.yaml: %v", err)
+	}
+
+	// Change to temp directory for the test
+	oldWd, _ := os.Getwd()
+	if err := os.Chdir(tmpDir); err != nil {
+		t.Fatalf("Failed to chdir: %v", err)
+	}
+	defer os.Chdir(oldWd)
+
+	// Test SetYamlConfig with aliased key (sync.branch should write as sync-branch)
+	if err := SetYamlConfig("sync.branch", "new-value"); err != nil {
+		t.Fatalf("SetYamlConfig() error = %v", err)
+	}
+
+	// Read back and verify
+	content, err := os.ReadFile(configPath)
+	if err != nil {
+		t.Fatalf("Failed to read config.yaml: %v", err)
+	}
+
+	contentStr := string(content)
+	// Should update the existing sync-branch line, not add sync.branch
+	if !strings.Contains(contentStr, "sync-branch: \"new-value\"") {
+		t.Errorf("config.yaml should contain 'sync-branch: \"new-value\"', got:\n%s", contentStr)
+	}
+	if strings.Contains(contentStr, "sync.branch") {
+		t.Errorf("config.yaml should NOT contain 'sync.branch' (should be normalized to sync-branch), got:\n%s", contentStr)
+	}
+}
+
 func TestSetYamlConfig(t *testing.T) {
 	// Create a temp directory with .beads/config.yaml
 	tmpDir, err := os.MkdirTemp("", "beads-yaml-test-*")