diff --git a/pkg/commands/git_commands/working_tree.go b/pkg/commands/git_commands/working_tree.go
index deb9e6a59..e4922a4f2 100644
--- a/pkg/commands/git_commands/working_tree.go
+++ b/pkg/commands/git_commands/working_tree.go
@@ -49,8 +49,10 @@ func (self *WorkingTreeCommands) StageFiles(paths []string, extraArgs []string)
 }
 
 // StageAll stages all files
-func (self *WorkingTreeCommands) StageAll() error {
-	cmdArgs := NewGitCmd("add").Arg("-A").ToArgv()
+func (self *WorkingTreeCommands) StageAll(onlyTrackedFiles bool) error {
+	cmdArgs := NewGitCmd("add").
+		ArgIfElse(onlyTrackedFiles, "-u", "-A").
+		ToArgv()
 
 	return self.cmd.New(cmdArgs).Run()
 }
diff --git a/pkg/gui/controllers/files_controller.go b/pkg/gui/controllers/files_controller.go
index 9f95c86f6..20567a510 100644
--- a/pkg/gui/controllers/files_controller.go
+++ b/pkg/gui/controllers/files_controller.go
@@ -634,7 +634,8 @@ func (self *FilesController) toggleStagedAllWithLock() error {
 			return err
 		}
 
-		if err := self.c.Git().WorkingTree.StageAll(); err != nil {
+		onlyTrackedFiles := self.context().GetFilter() == filetree.DisplayTracked
+		if err := self.c.Git().WorkingTree.StageAll(onlyTrackedFiles); err != nil {
 			return err
 		}
 	} else {
diff --git a/pkg/gui/controllers/helpers/fixup_helper.go b/pkg/gui/controllers/helpers/fixup_helper.go
index 37a0cf688..f44c23da8 100644
--- a/pkg/gui/controllers/helpers/fixup_helper.go
+++ b/pkg/gui/controllers/helpers/fixup_helper.go
@@ -133,7 +133,7 @@ func (self *FixupHelper) HandleFindBaseCommitForFixupPress() error {
 		Prompt: self.c.Tr.HunksWithOnlyAddedLinesWarning,
 		HandleConfirm: func() error {
 			if !hasStagedChanges {
-				if err := self.c.Git().WorkingTree.StageAll(); err != nil {
+				if err := self.c.Git().WorkingTree.StageAll(true); err != nil {
 					return err
 				}
 				self.c.Refresh(types.RefreshOptions{Mode: types.SYNC, Scope: []types.RefreshableView{types.FILES}})
diff --git a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
index 82bef8fd2..fbe59caa6 100644
--- a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
+++ b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
@@ -244,7 +244,7 @@ func (self *MergeAndRebaseHelper) PromptToContinueRebase() error {
 					Prompt: self.c.Tr.UnstagedFilesAfterConflictsResolved,
 					HandleConfirm: func() error {
 						self.c.LogAction(self.c.Tr.Actions.StageAllFiles)
-						if err := self.c.Git().WorkingTree.StageAll(); err != nil {
+						if err := self.c.Git().WorkingTree.StageAll(true); 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 33620acd6..e7bc74fa9 100644
--- a/pkg/gui/controllers/helpers/working_tree_helper.go
+++ b/pkg/gui/controllers/helpers/working_tree_helper.go
@@ -207,7 +207,7 @@ func (self *WorkingTreeHelper) promptToStageAllAndRetry(retry func() error) erro
 		Prompt: self.c.Tr.NoFilesStagedPrompt,
 		HandleConfirm: func() error {
 			self.c.LogAction(self.c.Tr.Actions.StageAllFiles)
-			if err := self.c.Git().WorkingTree.StageAll(); err != nil {
+			if err := self.c.Git().WorkingTree.StageAll(false); err != nil {
 				return err
 			}
 			self.syncRefresh()
@@ -228,7 +228,7 @@ func (self *WorkingTreeHelper) prepareFilesForCommit() error {
 	noStagedFiles := !self.AnyStagedFiles()
 	if noStagedFiles && self.c.UserConfig().Gui.SkipNoStagedFilesWarning {
 		self.c.LogAction(self.c.Tr.Actions.StageAllFiles)
-		err := self.c.Git().WorkingTree.StageAll()
+		err := self.c.Git().WorkingTree.StageAll(false)
 		if err != nil {
 			return err
 		}
diff --git a/pkg/integration/tests/filter_and_search/stage_all_stages_only_tracked_files_in_tracked_only_filter.go b/pkg/integration/tests/filter_and_search/stage_all_stages_only_tracked_files_in_tracked_only_filter.go
index aa812c50e..004cb5eb7 100644
--- a/pkg/integration/tests/filter_and_search/stage_all_stages_only_tracked_files_in_tracked_only_filter.go
+++ b/pkg/integration/tests/filter_and_search/stage_all_stages_only_tracked_files_in_tracked_only_filter.go
@@ -48,10 +48,7 @@ var StageAllStagesOnlyTrackedFilesInTrackedOnlyFilter = NewIntegrationTest(NewIn
 			Lines(
 				Equals("▼ /").IsSelected(),
 				Equals("  M  file-tracked"), // 'M' is now in the left column, so file is staged
-				/* EXPECTED:
 				Equals("  ?? file-untracked"),
-				ACTUAL: */
-				Equals("  A  file-untracked"),
 			)
 	},
 })