diff --git a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
index 7d4f0a96a..7f51bc35d 100644
--- a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
+++ b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
@@ -237,14 +237,14 @@ func (self *MergeAndRebaseHelper) PromptToContinueRebase() error {
 				Mode: types.SYNC, Scope: []types.RefreshableView{types.FILES},
 			})
 
-			root := self.c.Contexts().Files.FileTreeViewModel.GetRoot()
-			if root.GetHasUnstagedChanges() {
+			unstagedFiles := GetUnstagedFilesExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
+			if len(unstagedFiles) > 0 {
 				self.c.Confirm(types.ConfirmOpts{
 					Title:  self.c.Tr.Continue,
 					Prompt: self.c.Tr.UnstagedFilesAfterConflictsResolved,
 					HandleConfirm: func() error {
 						self.c.LogAction(self.c.Tr.Actions.StageAllFiles)
-						if err := self.c.Git().WorkingTree.StageAll(true); err != nil {
+						if err := self.c.Git().WorkingTree.StageFiles(unstagedFiles, []string{}); err != nil {
 							return err
 						}
 
diff --git a/pkg/gui/controllers/helpers/working_tree_helper.go b/pkg/gui/controllers/helpers/working_tree_helper.go
index 94a24e5ee..d6289537b 100644
--- a/pkg/gui/controllers/helpers/working_tree_helper.go
+++ b/pkg/gui/controllers/helpers/working_tree_helper.go
@@ -97,6 +97,12 @@ func IsWorkingTreeDirtyExceptSubmodules(files []*models.File, submoduleConfigs [
 	return AnyStagedFilesExceptSubmodules(files, submoduleConfigs) || AnyTrackedFilesExceptSubmodules(files, submoduleConfigs)
 }
 
+func GetUnstagedFilesExceptSubmodules(files []*models.File, submoduleConfigs []*models.SubmoduleConfig) []string {
+	return lo.FilterMap(files, func(f *models.File, _ int) (string, bool) {
+		return f.Path, f.HasUnstagedChanges && f.Tracked && !f.IsSubmodule(submoduleConfigs)
+	})
+}
+
 func (self *WorkingTreeHelper) FileForSubmodule(submodule *models.SubmoduleConfig) *models.File {
 	for _, file := range self.c.Model().Files {
 		if file.IsSubmodule([]*models.SubmoduleConfig{submodule}) {
diff --git a/pkg/integration/tests/branch/rebase_conflicts_fix_build_errors_with_out_of_date_submodule.go b/pkg/integration/tests/branch/rebase_conflicts_fix_build_errors_with_out_of_date_submodule.go
index 22fbfdb5f..1b95fd316 100644
--- a/pkg/integration/tests/branch/rebase_conflicts_fix_build_errors_with_out_of_date_submodule.go
+++ b/pkg/integration/tests/branch/rebase_conflicts_fix_build_errors_with_out_of_date_submodule.go
@@ -90,12 +90,9 @@ var RebaseConflictsFixBuildErrorsWithOutOfDateSubmodule = NewIntegrationTest(New
 
 		t.Views().Files().
 			Lines(
-				/* EXPECTED:
 				Equals("▼ /").IsSelected(),
 				Equals("   M submodule (submodule)"),
 				Equals("  ?? untracked-file"),
-				ACTUAL: */
-				Equals("?? untracked-file"),
 			)
 
 		t.Views().Commits().
@@ -109,10 +106,7 @@ var RebaseConflictsFixBuildErrorsWithOutOfDateSubmodule = NewIntegrationTest(New
 
 		t.Views().Main().
 			Content(
-				/* EXPECTED:
 				DoesNotContain("submodule").DoesNotContain("untracked-file"),
-				ACTUAL: */
-				Contains("submodule").DoesNotContain("untracked-file"),
 			)
 	},
 })