diff --git a/custom/conf/app.example.ini b/custom/conf/app.example.ini
index fffd6eeb72..548c39d4b6 100644
--- a/custom/conf/app.example.ini
+++ b/custom/conf/app.example.ini
@@ -762,7 +762,12 @@ LEVEL = Info
 
 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 ;; Git config options
-;; This section only does "set" config, a removed config key from this section won't be removed from git config automatically. The format is `some.configKey = value`.
+;; The format is `some.configKey = value`.
+;; These options will be written into the gitconfig file under "[git] HOME_PATH" when Gitea web starts.
+;; ATTENTION:
+;; * It only does "set" config, a removed config key from this section won't be removed from git config automatically.
+;; * Some config options might affect the behavior of git and fail Gitea's git operation,
+;;   make sure you know what you are doing before making changes.
 ;[git.config]
 ;diff.algorithm = histogram
 ;core.logAllRefUpdates = true
diff --git a/modules/git/config.go b/modules/git/config.go
index e6a2ac8817..b7f41251f8 100644
--- a/modules/git/config.go
+++ b/modules/git/config.go
@@ -21,14 +21,6 @@ func syncGitConfig(ctx context.Context) (err error) {
 		return fmt.Errorf("unable to prepare git home directory %s, err: %w", gitcmd.HomeDir(), err)
 	}
 
-	// first, write user's git config options to git config file
-	// user config options could be overwritten by builtin values later, because if a value is builtin, it must have some special purposes
-	for k, v := range setting.GitConfig.Options {
-		if err = configSet(ctx, strings.ToLower(k), v); err != nil {
-			return err
-		}
-	}
-
 	// Git requires setting user.name and user.email in order to commit changes - old comment: "if they're not set just add some defaults"
 	// TODO: need to confirm whether users really need to change these values manually. It seems that these values are dummy only and not really used.
 	// If these values are not really used, then they can be set (overwritten) directly without considering about existence.
@@ -111,8 +103,18 @@ func syncGitConfig(ctx context.Context) (err error) {
 		}
 		err = configUnsetAll(ctx, "uploadpack.allowAnySHA1InWant", "true")
 	}
+	if err != nil {
+		return err
+	}
 
-	return err
+	// Apply user's git config options last so they take precedence over builtin defaults
+	for k, v := range setting.GitConfig.Options {
+		if err = configSet(ctx, strings.ToLower(k), v); err != nil {
+			return err
+		}
+	}
+
+	return nil
 }
 
 func configSet(ctx context.Context, key, value string) error {
diff --git a/modules/git/config_test.go b/modules/git/config_test.go
index 9e358d4a80..cdfca656e1 100644
--- a/modules/git/config_test.go
+++ b/modules/git/config_test.go
@@ -10,6 +10,7 @@ import (
 
 	"gitea.dev/modules/git/gitcmd"
 	"gitea.dev/modules/setting"
+	"gitea.dev/modules/test"
 
 	"github.com/stretchr/testify/assert"
 )
@@ -55,14 +56,18 @@ func TestGitConfig(t *testing.T) {
 	assert.False(t, gitConfigContains("key-x = *"))
 }
 
-func TestSyncConfig(t *testing.T) {
-	oldGitConfig := setting.GitConfig
-	defer func() {
-		setting.GitConfig = oldGitConfig
-	}()
+func TestSyncGitConfig(t *testing.T) {
+	defer test.MockVariableValue(&setting.GitConfig)()
+
+	assert.Empty(t, setting.GitConfig.Options)
+	assert.NoError(t, syncGitConfig(t.Context()))
+	assert.True(t, gitConfigContains("commitGraph = true")) // builtin default config
 
 	setting.GitConfig.Options["sync-test.cfg-key-a"] = "CfgValA"
+	setting.GitConfig.Options["core.commitgraph"] = "false"
 	assert.NoError(t, syncGitConfig(t.Context()))
 	assert.True(t, gitConfigContains("[sync-test]"))
 	assert.True(t, gitConfigContains("cfg-key-a = CfgValA"))
+	assert.False(t, gitConfigContains("commitGraph"))        // builtin default config can be overridden
+	assert.True(t, gitConfigContains("commitgraph = false")) // git config key is case-insensitive
 }