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
new file mode 100644
index 000000000..1b95fd316
--- /dev/null
+++ b/pkg/integration/tests/branch/rebase_conflicts_fix_build_errors_with_out_of_date_submodule.go
@@ -0,0 +1,112 @@
+package branch
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+	"github.com/jesseduffield/lazygit/pkg/integration/tests/shared"
+)
+
+var RebaseConflictsFixBuildErrorsWithOutOfDateSubmodule = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Rebase onto another branch, deal with the conflicts. While continue prompt is showing, fix build errors; get another prompt when continuing. Check that we don't stage submodules here.",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig: func(config *config.AppConfig) {
+		config.GetUserConfig().Git.LocalBranchSortOrder = "recency"
+	},
+	SetupRepo: func(shell *Shell) {
+		// Create an out-of-date submodule to verify that we don't try to stage it
+		shell.
+			EmptyCommit("Initial commit").
+			CloneIntoSubmodule("submodule", "submodule").
+			Commit("Add submodule").
+			AddFileInWorktreeOrSubmodule("submodule", "file", "content").
+			CommitInWorktreeOrSubmodule("submodule", "add file in submodule")
+
+		shared.MergeConflictsSetup(shell)
+
+		// Create an untracked file to verify that we don't try to stage it either
+		shell.UpdateFile("untracked-file", "some untracked file")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Commits().TopLines(
+			Contains("first change"),
+			Contains("original"),
+		)
+
+		t.Views().Branches().
+			Focus().
+			Lines(
+				Contains("first-change-branch"),
+				Contains("second-change-branch"),
+				Contains("original-branch"),
+				Contains("master"),
+			).
+			SelectNextItem().
+			Press(keys.Branches.RebaseBranch)
+
+		t.ExpectPopup().Menu().
+			Title(Equals("Rebase 'first-change-branch'")).
+			Select(Contains("Simple rebase")).
+			Confirm()
+
+		t.Common().AcknowledgeConflicts()
+
+		t.Views().Files().
+			IsFocused().
+			SelectedLine(Contains("file")).
+			PressEnter()
+
+		t.Views().MergeConflicts().
+			IsFocused().
+			SelectNextItem().
+			PressPrimaryAction()
+
+		t.Views().Information().Content(Contains("Rebasing"))
+
+		popup := t.ExpectPopup().Confirmation().
+			Title(Equals("Continue")).
+			Content(Contains("All merge conflicts resolved. Continue the rebase?"))
+
+		// While the popup is showing, fix some build errors
+		t.Shell().UpdateFile("file", "make it compile again")
+
+		// Continue
+		popup.Confirm()
+
+		t.Views().Files().
+			Lines(
+				Equals("▼ /").IsSelected(),
+				Equals("  MM file"),
+				Equals("   M submodule (submodule)"),
+				Equals("  ?? untracked-file"),
+			)
+
+		t.ExpectPopup().Confirmation().
+			Title(Equals("Continue")).
+			Content(Contains("Files have been modified since conflicts were resolved. Auto-stage them and continue?")).
+			Confirm()
+
+		t.Views().Information().Content(DoesNotContain("Rebasing"))
+
+		t.Views().Files().
+			Lines(
+				Equals("▼ /").IsSelected(),
+				Equals("   M submodule (submodule)"),
+				Equals("  ?? untracked-file"),
+			)
+
+		t.Views().Commits().
+			Focus().
+			TopLines(
+				Contains("first change").IsSelected(),
+				Contains("second-change-branch unrelated change"),
+				Contains("second change"),
+				Contains("original"),
+			)
+
+		t.Views().Main().
+			Content(
+				DoesNotContain("submodule").DoesNotContain("untracked-file"),
+			)
+	},
+})
diff --git a/pkg/integration/tests/test_list.go b/pkg/integration/tests/test_list.go
index 3d8edfb56..7f228635a 100644
--- a/pkg/integration/tests/test_list.go
+++ b/pkg/integration/tests/test_list.go
@@ -69,6 +69,7 @@ var tests = []*components.IntegrationTest{
 	branch.RebaseAndDrop,
 	branch.RebaseCancelOnConflict,
 	branch.RebaseConflictsFixBuildErrors,
+	branch.RebaseConflictsFixBuildErrorsWithOutOfDateSubmodule,
 	branch.RebaseCopiedBranch,
 	branch.RebaseDoesNotAutosquash,
 	branch.RebaseFromMarkedBase,