diff --git a/pkg/gui/controllers/working_tree_diff_actions.go b/pkg/gui/controllers/working_tree_diff_actions.go
index 6feae8380..d0130ae49 100644
--- a/pkg/gui/controllers/working_tree_diff_actions.go
+++ b/pkg/gui/controllers/working_tree_diff_actions.go
@@ -171,6 +171,19 @@ func (self *WorkingTreeDiffActions) applyDiffLines(
 		}
 	}
 
+	// Acting on every change of a file is acting on the file itself, and saying so is
+	// not the same as applying its diff. The diff of a deleted file is its content
+	// going away, and putting that into the index line by line leaves an empty file
+	// there rather than the deletion; the diff of an added one is its whole content,
+	// and taking that back out leaves an empty file in the index rather than an
+	// untracked one.
+	if opts.Cached && len(patchLineIndices) == changeLineCount(parsedPatch) {
+		if opts.Reverse {
+			return self.c.Git().WorkingTree.UnStageFile(file.Names(), file.Tracked)
+		}
+		return self.c.Git().WorkingTree.StageFile(file.GetPath())
+	}
+
 	patchToApply := parsedPatch.
 		Transform(patch.TransformOpts{
 			Reverse:             opts.Reverse,
@@ -184,3 +197,11 @@ func (self *WorkingTreeDiffActions) applyDiffLines(
 
 	return self.c.Git().Patch.ApplyPatch(patchToApply, opts)
 }
+
+// changeLineCount returns how many of a patch's lines are changes rather than context
+// or header. A selection of the whole diff covers exactly that many.
+func changeLineCount(p *patch.Patch) int {
+	return lo.CountBy(p.Lines(), func(line *patch.PatchLine) bool {
+		return line.IsAddition() || line.IsDeletion()
+	})
+}
diff --git a/pkg/integration/tests/main_view/stage_deleted_file.go b/pkg/integration/tests/main_view/stage_deleted_file.go
new file mode 100644
index 000000000..9b863ae72
--- /dev/null
+++ b/pkg/integration/tests/main_view/stage_deleted_file.go
@@ -0,0 +1,80 @@
+package main_view
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var StageDeletedFile = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Acting on the whole of a file's block in a directory's diff acts on the file: staging a deletion, and unstaging an addition",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig: func(cfg *config.AppConfig) {
+		cfg.GetUserConfig().Gui.UseHunkModeInStagingView = false
+	},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateFileAndAdd("fileA", "a\n")
+		shell.CreateFileAndAdd("fileB", "b1\nb2\n")
+		shell.Commit("one")
+
+		shell.UpdateFile("fileA", "a\nfromA\n")
+		shell.DeleteFile("fileB")
+		shell.CreateFileAndAdd("fileC", "c1\nc2\n")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Contains("▼ /").IsSelected(),
+				Contains(" M fileA"),
+				Contains(" D fileB"),
+				Contains("A  fileC"),
+			).
+			Press(keys.Universal.FocusMainView)
+
+		// Select everything the deleted file contributes to the diff.
+		t.Views().Main().
+			IsFocused().
+			NavigateToLine(Contains("-b1")).
+			Press(keys.Universal.ToggleRangeSelect).
+			NavigateToLine(Contains("-b2")).
+			SelectedLines(
+				Contains("-b1"),
+				Contains("-b2"),
+			).
+			PressPrimaryAction()
+
+		// The file is staged as deleted. Applying its lines as a patch would have left
+		// an empty file in the index instead, which is not what deleting a file means.
+		t.Views().Files().Lines(
+			Contains("▼ /"),
+			Contains(" M fileA"),
+			Contains("D  fileB"),
+			Contains("A  fileC"),
+		)
+
+		// The same the other way round: taking the whole of an added file back out of
+		// the index leaves it untracked, rather than tracked and empty.
+		t.Views().Main().
+			IsFocused().
+			Press(keys.Universal.TogglePanel)
+
+		t.Views().Secondary().
+			IsFocused().
+			NavigateToLine(Contains("+c1")).
+			Press(keys.Universal.ToggleRangeSelect).
+			NavigateToLine(Contains("+c2")).
+			SelectedLines(
+				Contains("+c1"),
+				Contains("+c2"),
+			).
+			PressPrimaryAction()
+
+		t.Views().Files().Lines(
+			Contains("▼ /"),
+			Contains(" M fileA"),
+			Contains("D  fileB"),
+			Contains("?? fileC"),
+		)
+	},
+})
diff --git a/pkg/integration/tests/test_list.go b/pkg/integration/tests/test_list.go
index 9a449c0e5..44350dcb8 100644
--- a/pkg/integration/tests/test_list.go
+++ b/pkg/integration/tests/test_list.go
@@ -408,6 +408,7 @@ var tests = []*components.IntegrationTest{
 	main_view.SelectVisibleHunkOnFocusingMainView,
 	main_view.SelectionCommandsOnlyWhereTheyApply,
 	main_view.SelectionOverTheCustomPatch,
+	main_view.StageDeletedFile,
 	main_view.StageDiffLines,
 	main_view.StageDiffLinesOfAPathWithASpace,
 	main_view.StageRangeSpanningFiles,