diff --git a/gitindex/clone.go b/gitindex/clone.go
index 2399e29fa..493abef64 100644
--- a/gitindex/clone.go
+++ b/gitindex/clone.go
@@ -22,30 +22,81 @@ import (
 	"os/exec"
 	"path/filepath"
 	"sort"
+	"strings"
 
 	git "github.com/go-git/go-git/v5"
 	"github.com/go-git/go-git/v5/config"
 )
 
+// returns a list of all the git zoekt settings that have changed or are
+// new. To do this it gets the current config, turns into into a map and diffs
+// against the new settings map
+func getZoektSettingsToUpdate(repoDest string, newSettings map[string]string, newSettingsKeys []string) ([]string, error) {
+	cmd := exec.Command("git", "-C", repoDest, "config", "--local", "--get-regexp", "zoekt")
+	outBuf := &bytes.Buffer{}
+	errBuf := &bytes.Buffer{}
+	cmd.Stdout = outBuf
+	cmd.Stderr = errBuf
+
+	if err := cmd.Run(); err != nil {
+		log.Printf("error getting settings\n")
+		return nil, err
+	}
+
+	// collect every current setting and put it into a map
+	oldSettings := make(map[string]string)
+	for _, cl := range bytes.Split(outBuf.Bytes(), []byte{'\n'}) {
+		if len(cl) == 0 {
+			continue
+		}
+
+		parts := bytes.SplitN(cl, []byte{' '}, 2)
+		if len(parts) != 2 {
+			return nil, fmt.Errorf("more parts than expected in git config key/v line")
+		}
+		oldSettings[string(parts[0])] = strings.TrimSpace(string(parts[1]))
+	}
+
+	// get the list of settings that have changed, or are new
+	var settingsToUpdate []string
+	for _, k := range newSettingsKeys {
+		oldVal, oldHasSetting := oldSettings[k]
+		if (!oldHasSetting && newSettings[k] != "") || oldVal != newSettings[k] {
+			settingsToUpdate = append(settingsToUpdate, k)
+		}
+	}
+
+	return settingsToUpdate, nil
+}
+
 // Updates the zoekt.* git config options after a repo is cloned.
 // Once a repo is cloned, we can no longer use the --config flag to update all
 // of it's zoekt.* settings at once. `git config` is limited to one option at once.
-func updateZoektGitConfig(repoDest string, settings map[string]string) error {
+func updateZoektGitConfig(repoDest string, settings map[string]string) (bool, error) {
 	var keys []string
 	for k := range settings {
 		keys = append(keys, k)
 	}
 	sort.Strings(keys)
 
-	for _, k := range keys {
+	settingsToUpdate, err := getZoektSettingsToUpdate(repoDest, settings, keys)
+	if err != nil {
+		return false, err
+	}
+
+	if len(settingsToUpdate) == 0 {
+		return false, nil
+	}
+
+	for _, k := range settingsToUpdate {
 		if settings[k] != "" {
 			if err := exec.Command("git", "-C", repoDest, "config", k, settings[k]).Run(); err != nil {
-				return err
+				return false, err
 			}
 		}
 	}
 
-	return nil
+	return true, nil
 }
 
 // CloneRepo clones one repository, adding the given config
@@ -61,9 +112,13 @@ func CloneRepo(destDir, name, cloneURL string, settings map[string]string) (stri
 	repoDest := filepath.Join(parent, filepath.Base(name)+".git")
 	if _, err := os.Lstat(repoDest); err == nil {
 		// Repository exists, ensure settings are in sync
-		if err := updateZoektGitConfig(repoDest, settings); err != nil {
+		hadUpdate, err := updateZoektGitConfig(repoDest, settings)
+		if err != nil {
 			return "", fmt.Errorf("failed to update repository settings: %w", err)
 		}
+		if hadUpdate {
+			return repoDest, nil
+		}
 		return "", nil
 	}