diff --git a/pkg/app/entry_point.go b/pkg/app/entry_point.go
index a3225e311..14e13a739 100644
--- a/pkg/app/entry_point.go
+++ b/pkg/app/entry_point.go
@@ -136,6 +136,25 @@ func Start(buildInfo *BuildInfo, integrationTest integrationTypes.IntegrationTes
 	}
 	defer os.RemoveAll(tempDir)
 
+	// When git invokes lazygit as a daemon (e.g. as the editor of a rebase todo
+	// file), skip loading and migrating the user config entirely; the daemon
+	// doesn't need it, and migrating the config here would dirty the working
+	// tree in the middle of the git operation (see #5998).
+	if daemon.InDaemonMode() {
+		appConfig, err := config.NewAppConfigForDaemon("lazygit", buildInfo.Version, buildInfo.Commit, buildInfo.Date, buildInfo.BuildSource, cliArgs.Debug, tempDir)
+		if err != nil {
+			log.Fatal(err.Error())
+		}
+
+		common, err := NewCommon(appConfig)
+		if err != nil {
+			log.Fatal(err)
+		}
+
+		daemon.Handle(common)
+		return
+	}
+
 	appConfig, err := config.NewAppConfig("lazygit", buildInfo.Version, buildInfo.Commit, buildInfo.Date, buildInfo.BuildSource, cliArgs.Debug, tempDir)
 	if err != nil {
 		log.Fatal(err.Error())
@@ -159,11 +178,6 @@ func Start(buildInfo *BuildInfo, integrationTest integrationTypes.IntegrationTes
 		log.Fatal(err)
 	}
 
-	if daemon.InDaemonMode() {
-		daemon.Handle(common)
-		return
-	}
-
 	if cliArgs.Profile {
 		go func() {
 			if err := http.ListenAndServe("localhost:6060", nil); err != nil {
diff --git a/pkg/config/app_config.go b/pkg/config/app_config.go
index ade614f7d..a041497af 100644
--- a/pkg/config/app_config.go
+++ b/pkg/config/app_config.go
@@ -130,6 +130,45 @@ func NewAppConfig(
 	return appConfig, nil
 }
 
+// NewAppConfigForDaemon makes a new app config for running lazygit in daemon
+// mode, i.e. when git invokes lazygit as e.g. the editor of a rebase todo
+// file. The daemon doesn't need the user config for anything, so it is neither
+// loaded nor migrated here: migrating the config from within a git operation
+// would modify the working tree mid-operation, aborting e.g. a rebase with
+// "error: Your local changes to the following files would be overwritten by
+// merge" when the config file is checked in (see #5998).
+func NewAppConfigForDaemon(
+	name string,
+	version,
+	commit,
+	date string,
+	buildSource string,
+	debuggingFlag bool,
+	tempDir string,
+) (*AppConfig, error) {
+	configDir, err := findOrCreateConfigDir()
+	if err != nil && !os.IsPermission(err) {
+		return nil, err
+	}
+
+	appState, err := loadAppState()
+	if err != nil {
+		return nil, err
+	}
+
+	return &AppConfig{
+		name:          name,
+		version:       version,
+		buildDate:     date,
+		debug:         debuggingFlag,
+		buildSource:   buildSource,
+		userConfig:    GetDefaultConfigForPlatform(KeybindingPlatform()),
+		userConfigDir: configDir,
+		tempDir:       tempDir,
+		appState:      appState,
+	}, nil
+}
+
 func ConfigDir() string {
 	_, filePath := findConfigFile(ConfigFilename)
 
diff --git a/pkg/config/app_config_daemon_test.go b/pkg/config/app_config_daemon_test.go
new file mode 100644
index 000000000..79bf88a43
--- /dev/null
+++ b/pkg/config/app_config_daemon_test.go
@@ -0,0 +1,41 @@
+package config
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+// Invoking lazygit as a daemon (e.g. as the editor of a rebase todo file) must
+// not load or migrate the user config: writing a migrated config back to disk
+// dirties the working tree in the middle of the git operation, aborting a
+// rebase whose repo has the config file checked in (see #5998).
+func TestNewAppConfigForDaemonDoesNotTouchUserConfig(t *testing.T) {
+	stateDir := t.TempDir()
+	t.Setenv("CONFIG_DIR", stateDir)
+
+	configPath := filepath.Join(stateDir, ConfigFilename)
+	preMigrationConfig := "git:\n  pagers:\n    - pager: less\n"
+	if err := os.WriteFile(configPath, []byte(preMigrationConfig), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	appConfig, err := NewAppConfigForDaemon("lazygit", "test-version", "test-commit", "test-date", "test-build", false, t.TempDir())
+	assert.NoError(t, err)
+	if appConfig == nil {
+		t.Fatal("expected non-nil app config")
+	}
+
+	// The config file must be untouched (not created, not migrated, not
+	// rewritten).
+	content, err := os.ReadFile(configPath)
+	assert.NoError(t, err)
+	assert.Equal(t, preMigrationConfig, string(content))
+
+	// The daemon still gets a usable config object with defaults, and usable
+	// app state.
+	assert.NotNil(t, appConfig.GetUserConfig())
+	assert.NotNil(t, appConfig.GetAppState())
+}