diff --git a/internal/config/config.go b/internal/config/config.go
index 6e2c91e..3160085 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -234,8 +234,8 @@ func LoadConfig() (*Config, error) {
 				continue
 			}
 
-			branchName := strings.ToLower(keyParts[2])
-			property := strings.ToLower(keyParts[3])
+			branchName := strings.ToLower(strings.Join(keyParts[2:len(keyParts)-1], "."))
+			property := strings.ToLower(keyParts[len(keyParts)-1])
 
 			// Initialize branch map if needed
 			if _, ok := branchMap[branchName]; !ok {
diff --git a/test/internal/config/config_test.go b/test/internal/config/config_test.go
index 1731d6b..f74c6eb 100644
--- a/test/internal/config/config_test.go
+++ b/test/internal/config/config_test.go
@@ -270,6 +270,58 @@ func TestApplyOverrides_CustomBranchNames(t *testing.T) {
 	assert.False(t, exists)
 }
 
+func TestApplyOverrides_CustomBranchNamesWithDots(t *testing.T) {
+	cfg := config.DefaultConfig()
+	cfg = config.ApplyOverrides(cfg, config.ConfigOverrides{
+		MainBranch:    "custom.main",
+		DevelopBranch: "custom.dev",
+	})
+
+	// Check main branch (base branch)
+	mainConfig, exists := cfg.Branches["custom.main"]
+	assert.True(t, exists)
+	assert.Equal(t, string(config.BranchTypeBase), mainConfig.Type)
+	assert.Equal(t, "", mainConfig.Parent)
+	assert.Equal(t, "", mainConfig.StartPoint)
+
+	// Check develop branch (base branch)
+	developConfig, exists := cfg.Branches["custom.dev"]
+	assert.True(t, exists)
+	assert.Equal(t, string(config.BranchTypeBase), developConfig.Type)
+	assert.Equal(t, "custom.main", developConfig.Parent)
+	assert.Equal(t, "", developConfig.StartPoint)
+
+	// Check feature branch parent and start point
+	featureConfig, exists := cfg.Branches["feature"]
+	assert.True(t, exists)
+	assert.Equal(t, "custom.dev", featureConfig.Parent)
+	assert.Equal(t, "custom.dev", featureConfig.StartPoint)
+
+	// Check release branch parent and start point
+	releaseConfig, exists := cfg.Branches["release"]
+	assert.True(t, exists)
+	assert.Equal(t, "custom.main", releaseConfig.Parent)
+	assert.Equal(t, "custom.dev", releaseConfig.StartPoint)
+
+	// Check hotfix branch parent and start point
+	hotfixConfig, exists := cfg.Branches["hotfix"]
+	assert.True(t, exists)
+	assert.Equal(t, "custom.main", hotfixConfig.Parent)
+	assert.Equal(t, "custom.main", hotfixConfig.StartPoint)
+
+	// Check support branch parent and start point
+	supportConfig, exists := cfg.Branches["support"]
+	assert.True(t, exists)
+	assert.Equal(t, "custom.main", supportConfig.Parent)
+	assert.Equal(t, "custom.main", supportConfig.StartPoint)
+
+	// Check old names don't exist
+	_, exists = cfg.Branches["main"]
+	assert.False(t, exists)
+	_, exists = cfg.Branches["develop"]
+	assert.False(t, exists)
+}
+
 func TestApplyOverrides_CustomPrefixes(t *testing.T) {
 	cfg := config.DefaultConfig()
 	cfg = config.ApplyOverrides(cfg, config.ConfigOverrides{