diff --git a/pkg/gui/controllers/custom_patch_options_menu_action.go b/pkg/gui/controllers/custom_patch_options_menu_action.go
index d6a36c2e1..793048429 100644
--- a/pkg/gui/controllers/custom_patch_options_menu_action.go
+++ b/pkg/gui/controllers/custom_patch_options_menu_action.go
@@ -173,7 +173,7 @@ func (self *CustomPatchOptionsMenuAction) handleMovePatchIntoWorkingTree() error
 
 	self.returnFocusFromPatchExplorerIfNecessary()
 
-	mustStash := self.c.Helpers().WorkingTree.IsWorkingTreeDirty()
+	mustStash := self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules()
 	return self.c.ConfirmIf(mustStash, types.ConfirmOpts{
 		Title:  self.c.Tr.MustStashTitle,
 		Prompt: self.c.Tr.MustStashWarning,
diff --git a/pkg/gui/controllers/files_controller.go b/pkg/gui/controllers/files_controller.go
index 4a3951c48..0289936de 100644
--- a/pkg/gui/controllers/files_controller.go
+++ b/pkg/gui/controllers/files_controller.go
@@ -973,7 +973,7 @@ func (self *FilesController) createStashMenu() error {
 			{
 				Label: self.c.Tr.StashAllChanges,
 				OnPress: func() error {
-					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirty() {
+					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules() {
 						return errors.New(self.c.Tr.NoFilesToStash)
 					}
 					return self.handleStashSave(self.c.Git().Stash.Push, self.c.Tr.Actions.StashAllChanges)
@@ -983,7 +983,7 @@ func (self *FilesController) createStashMenu() error {
 			{
 				Label: self.c.Tr.StashAllChangesKeepIndex,
 				OnPress: func() error {
-					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirty() {
+					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules() {
 						return errors.New(self.c.Tr.NoFilesToStash)
 					}
 					// if there are no staged files it behaves the same as Stash.Save
@@ -1002,7 +1002,7 @@ func (self *FilesController) createStashMenu() error {
 				Label: self.c.Tr.StashStagedChanges,
 				OnPress: func() error {
 					// there must be something in staging otherwise the current implementation mucks the stash up
-					if !self.c.Helpers().WorkingTree.AnyStagedFiles() {
+					if !self.c.Helpers().WorkingTree.AnyStagedFilesExceptSubmodules() {
 						return errors.New(self.c.Tr.NoTrackedStagedFilesStash)
 					}
 					return self.handleStashSave(self.c.Git().Stash.SaveStagedChanges, self.c.Tr.Actions.StashStagedChanges)
@@ -1012,10 +1012,10 @@ func (self *FilesController) createStashMenu() error {
 			{
 				Label: self.c.Tr.StashUnstagedChanges,
 				OnPress: func() error {
-					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirty() {
+					if !self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules() {
 						return errors.New(self.c.Tr.NoFilesToStash)
 					}
-					if self.c.Helpers().WorkingTree.AnyStagedFiles() {
+					if self.c.Helpers().WorkingTree.AnyStagedFilesExceptSubmodules() {
 						return self.handleStashSave(self.c.Git().Stash.StashUnstagedChanges, self.c.Tr.Actions.StashUnstagedChanges)
 					}
 					// ordinary stash
diff --git a/pkg/gui/controllers/helpers/cherry_pick_helper.go b/pkg/gui/controllers/helpers/cherry_pick_helper.go
index 8f5b37a66..c4be07ceb 100644
--- a/pkg/gui/controllers/helpers/cherry_pick_helper.go
+++ b/pkg/gui/controllers/helpers/cherry_pick_helper.go
@@ -77,7 +77,7 @@ func (self *CherryPickHelper) Paste() error {
 			}),
 		HandleConfirm: func() error {
 			return self.c.WithWaitingStatusSync(self.c.Tr.CherryPickingStatus, func() error {
-				mustStash := IsWorkingTreeDirty(self.c.Model().Files)
+				mustStash := IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
 
 				self.c.LogAction(self.c.Tr.Actions.CherryPick)
 
diff --git a/pkg/gui/controllers/helpers/refs_helper.go b/pkg/gui/controllers/helpers/refs_helper.go
index cfb9d3bab..39cda5bd4 100644
--- a/pkg/gui/controllers/helpers/refs_helper.go
+++ b/pkg/gui/controllers/helpers/refs_helper.go
@@ -258,7 +258,7 @@ func (self *RefsHelper) CreateGitResetMenu(name string, ref string) error {
 				style.FgRed.Sprintf("reset --%s %s", row.strength, name),
 			},
 			OnPress: func() error {
-				return self.c.ConfirmIf(row.strength == "hard" && IsWorkingTreeDirty(self.c.Model().Files),
+				return self.c.ConfirmIf(row.strength == "hard" && IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules),
 					types.ConfirmOpts{
 						Title:  self.c.Tr.Actions.HardReset,
 						Prompt: self.c.Tr.ResetHardConfirmation,
@@ -484,7 +484,7 @@ func (self *RefsHelper) moveCommitsToNewBranchStackedOnCurrentBranch(newBranchNa
 		return err
 	}
 
-	mustStash := IsWorkingTreeDirty(self.c.Model().Files)
+	mustStash := IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
 	if mustStash {
 		if err := self.c.Git().Stash.Push(fmt.Sprintf(self.c.Tr.AutoStashForNewBranch, newBranchName)); err != nil {
 			return err
@@ -517,7 +517,7 @@ func (self *RefsHelper) moveCommitsToNewBranchOffOfMainBranch(newBranchName stri
 		return commit.Status == models.StatusUnpushed
 	})
 
-	mustStash := IsWorkingTreeDirty(self.c.Model().Files)
+	mustStash := IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
 	if mustStash {
 		if err := self.c.Git().Stash.Push(fmt.Sprintf(self.c.Tr.AutoStashForNewBranch, newBranchName)); 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 9e6e36296..6437afa35 100644
--- a/pkg/gui/controllers/helpers/working_tree_helper.go
+++ b/pkg/gui/controllers/helpers/working_tree_helper.go
@@ -47,6 +47,14 @@ func AnyStagedFiles(files []*models.File) bool {
 	return lo.SomeBy(files, func(f *models.File) bool { return f.HasStagedChanges })
 }
 
+func (self *WorkingTreeHelper) AnyStagedFilesExceptSubmodules() bool {
+	return AnyStagedFilesExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
+}
+
+func AnyStagedFilesExceptSubmodules(files []*models.File, submoduleConfigs []*models.SubmoduleConfig) bool {
+	return lo.SomeBy(files, func(f *models.File) bool { return f.HasStagedChanges && !f.IsSubmodule(submoduleConfigs) })
+}
+
 func (self *WorkingTreeHelper) AnyTrackedFiles() bool {
 	return AnyTrackedFiles(self.c.Model().Files)
 }
@@ -55,12 +63,20 @@ func AnyTrackedFiles(files []*models.File) bool {
 	return lo.SomeBy(files, func(f *models.File) bool { return f.Tracked })
 }
 
-func (self *WorkingTreeHelper) IsWorkingTreeDirty() bool {
-	return IsWorkingTreeDirty(self.c.Model().Files)
+func (self *WorkingTreeHelper) AnyTrackedFilesExceptSubmodules() bool {
+	return AnyTrackedFilesExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
 }
 
-func IsWorkingTreeDirty(files []*models.File) bool {
-	return AnyStagedFiles(files) || AnyTrackedFiles(files)
+func AnyTrackedFilesExceptSubmodules(files []*models.File, submoduleConfigs []*models.SubmoduleConfig) bool {
+	return lo.SomeBy(files, func(f *models.File) bool { return f.Tracked && !f.IsSubmodule(submoduleConfigs) })
+}
+
+func (self *WorkingTreeHelper) IsWorkingTreeDirtyExceptSubmodules() bool {
+	return IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
+}
+
+func IsWorkingTreeDirtyExceptSubmodules(files []*models.File, submoduleConfigs []*models.SubmoduleConfig) bool {
+	return AnyStagedFilesExceptSubmodules(files, submoduleConfigs) || AnyTrackedFilesExceptSubmodules(files, submoduleConfigs)
 }
 
 func (self *WorkingTreeHelper) FileForSubmodule(submodule *models.SubmoduleConfig) *models.File {
diff --git a/pkg/gui/controllers/local_commits_controller.go b/pkg/gui/controllers/local_commits_controller.go
index b70a4ecb9..9badaf1ed 100644
--- a/pkg/gui/controllers/local_commits_controller.go
+++ b/pkg/gui/controllers/local_commits_controller.go
@@ -856,7 +856,7 @@ func (self *LocalCommitsController) revert(commits []*models.Commit, start, end
 		HandleConfirm: func() error {
 			self.c.LogAction(self.c.Tr.Actions.RevertCommit)
 			return self.c.WithWaitingStatusSync(self.c.Tr.RevertingStatus, func() error {
-				mustStash := helpers.IsWorkingTreeDirty(self.c.Model().Files)
+				mustStash := helpers.IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules)
 
 				if mustStash {
 					if err := self.c.Git().Stash.Push(self.c.Tr.AutoStashForReverting); err != nil {
diff --git a/pkg/gui/controllers/undo_controller.go b/pkg/gui/controllers/undo_controller.go
index cd3b04e4f..cdc8a1280 100644
--- a/pkg/gui/controllers/undo_controller.go
+++ b/pkg/gui/controllers/undo_controller.go
@@ -257,7 +257,7 @@ func (self *UndoController) hardResetWithAutoStash(commitHash string, options ha
 	}
 
 	// if we have any modified tracked files we need to auto-stash
-	dirtyWorkingTree := self.c.Helpers().WorkingTree.IsWorkingTreeDirty()
+	dirtyWorkingTree := self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules()
 	if dirtyWorkingTree {
 		return self.c.WithWaitingStatus(options.WaitingStatus, func(gocui.Task) error {
 			if err := self.c.Git().Stash.Push(fmt.Sprintf(self.c.Tr.AutoStashForUndo, utils.ShortHash(commitHash))); err != nil {
diff --git a/pkg/gui/controllers/workspace_reset_controller.go b/pkg/gui/controllers/workspace_reset_controller.go
index de6fc4577..82357922f 100644
--- a/pkg/gui/controllers/workspace_reset_controller.go
+++ b/pkg/gui/controllers/workspace_reset_controller.go
@@ -100,7 +100,7 @@ func (self *FilesController) createResetMenu() error {
 			Tooltip: self.c.Tr.DiscardStagedChangesDescription,
 			OnPress: func() error {
 				self.c.LogAction(self.c.Tr.Actions.RemoveStagedFiles)
-				if !self.c.Helpers().WorkingTree.IsWorkingTreeDirty() {
+				if !self.c.Helpers().WorkingTree.IsWorkingTreeDirtyExceptSubmodules() {
 					return errors.New(self.c.Tr.NoTrackedStagedFilesStash)
 				}
 				if err := self.c.Git().Stash.SaveStagedChanges("[lazygit] tmp stash"); err != nil {
@@ -159,7 +159,7 @@ func (self *FilesController) createResetMenu() error {
 				red.Sprint("git reset --hard HEAD"),
 			},
 			OnPress: func() error {
-				return self.c.ConfirmIf(helpers.IsWorkingTreeDirty(self.c.Model().Files),
+				return self.c.ConfirmIf(helpers.IsWorkingTreeDirtyExceptSubmodules(self.c.Model().Files, self.c.Model().Submodules),
 					types.ConfirmOpts{
 						Title:  self.c.Tr.Actions.HardReset,
 						Prompt: self.c.Tr.ResetHardConfirmation,