diff --git a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
index 536c254dd..2b7f9cd16 100644
--- a/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
+++ b/pkg/gui/controllers/helpers/merge_and_rebase_helper.go
@@ -113,6 +113,7 @@ func (self *MergeAndRebaseHelper) genericMergeCommand(command string) error {
 			Mode:            types.ASYNC,
 			CommitSelection: commitSelectionAfterMerge(success && selectHeadCommitOnSuccess),
 		})
+		self.RecordWhetherMergeOrRebaseStartedInLazygit()
 		return err
 	}
 	result := self.c.Git().Rebase.GenericMergeOrRebaseAction(commandType, command)
@@ -165,9 +166,21 @@ func isMergeConflictErr(errStr string) bool {
 	return false
 }
 
+// RecordWhetherMergeOrRebaseStartedInLazygit is called right after we run a
+// merge/rebase/cherry-pick/revert step. If it left an operation in progress,
+// that operation is one we started, which is what later lets us auto-prompt to
+// continue it once its conflicts are resolved. If nothing is in progress
+// anymore (the step completed or aborted the operation), we clear the flag.
+func (self *MergeAndRebaseHelper) RecordWhetherMergeOrRebaseStartedInLazygit() {
+	self.c.State().GetRepoState().SetMergeOrRebaseStartedInLazygit(
+		self.c.Git().Status.WorkingTreeState().Any())
+}
+
 func (self *MergeAndRebaseHelper) CheckMergeOrRebaseWithRefreshOptions(result error, refreshOptions types.RefreshOptions) error {
 	self.c.Refresh(refreshOptions)
 
+	self.RecordWhetherMergeOrRebaseStartedInLazygit()
+
 	if result == nil {
 		return nil
 	} else if strings.Contains(result.Error(), "No changes - did you forget to use") {
diff --git a/pkg/gui/controllers/helpers/refresh_helper.go b/pkg/gui/controllers/helpers/refresh_helper.go
index 605309f9f..e40e0acd5 100644
--- a/pkg/gui/controllers/helpers/refresh_helper.go
+++ b/pkg/gui/controllers/helpers/refresh_helper.go
@@ -806,7 +806,16 @@ func (self *RefreshHelper) refreshStateFiles(background bool) error {
 		}
 	}
 
-	if self.c.Git().Status.WorkingTreeState().Any() && conflictFileCount == 0 && prevConflictFileCount > 0 {
+	repoState := self.c.State().GetRepoState()
+	if self.c.Git().Status.WorkingTreeState().None() {
+		// No operation is in progress (any more), so forget that we started one.
+		// This also covers an operation that was finished or aborted externally.
+		repoState.SetMergeOrRebaseStartedInLazygit(false)
+	} else if conflictFileCount == 0 && prevConflictFileCount > 0 && repoState.GetMergeOrRebaseStartedInLazygit() {
+		// The conflicts of an operation we started have just been resolved (e.g.
+		// in the user's editor). Offer to continue it. We only do this for
+		// operations we started ourselves; prompting for one that was started
+		// outside lazygit (e.g. by a coding agent) would be confusing.
 		self.c.OnUIThread(func() error { return self.mergeAndRebaseHelper.PromptToContinueRebase() })
 	}
 
diff --git a/pkg/gui/gui.go b/pkg/gui/gui.go
index dfc71d642..08d560ce5 100644
--- a/pkg/gui/gui.go
+++ b/pkg/gui/gui.go
@@ -255,6 +255,14 @@ type GuiRepoState struct {
 	CurrentPopupOpts *types.CreatePopupPanelOpts
 
 	LastBackgroundFetchTime time.Time
+
+	// Whether the rebase/merge/cherry-pick/revert that's currently in progress
+	// was started from within lazygit (as opposed to being started externally,
+	// e.g. in another terminal or by a coding agent). We only auto-prompt to
+	// continue such an operation once its conflicts are resolved if we started
+	// it ourselves; for an externally started one, popping up unbidden would be
+	// confusing. Reset whenever we observe that no operation is in progress.
+	mergeOrRebaseStartedInLazygit bool
 }
 
 var _ types.IRepoStateAccessor = new(GuiRepoState)
@@ -283,6 +291,14 @@ func (self *GuiRepoState) SetCurrentPopupOpts(value *types.CreatePopupPanelOpts)
 	self.CurrentPopupOpts = value
 }
 
+func (self *GuiRepoState) GetMergeOrRebaseStartedInLazygit() bool {
+	return self.mergeOrRebaseStartedInLazygit
+}
+
+func (self *GuiRepoState) SetMergeOrRebaseStartedInLazygit(value bool) {
+	self.mergeOrRebaseStartedInLazygit = value
+}
+
 func (self *GuiRepoState) GetScreenMode() types.ScreenMode {
 	return self.ScreenMode
 }
diff --git a/pkg/gui/gui_driver.go b/pkg/gui/gui_driver.go
index 57425231a..fef33bf66 100644
--- a/pkg/gui/gui_driver.go
+++ b/pkg/gui/gui_driver.go
@@ -68,6 +68,15 @@ func (self *GuiDriver) FocusIn() {
 	self.waitTillIdle()
 }
 
+func (self *GuiDriver) PretendMergeOrRebaseStartedInLazygit() {
+	self.gui.onUIThread(func() error {
+		self.gui.State.SetMergeOrRebaseStartedInLazygit(true)
+		return nil
+	})
+
+	self.waitTillIdle()
+}
+
 // wait until lazygit is idle (i.e. all processing is done) before continuing
 func (self *GuiDriver) waitTillIdle() {
 	<-self.isIdleChan
diff --git a/pkg/gui/services/custom_commands/handler_creator.go b/pkg/gui/services/custom_commands/handler_creator.go
index 19694c481..1e321c2de 100644
--- a/pkg/gui/services/custom_commands/handler_creator.go
+++ b/pkg/gui/services/custom_commands/handler_creator.go
@@ -318,6 +318,10 @@ func (self *HandlerCreator) finalHandler(customCommand config.CustomCommand, ses
 
 		if err != nil {
 			if customCommand.After != nil && customCommand.After.CheckForConflicts {
+				// The custom command may have started a rebase/merge/etc.; if so,
+				// it's one we consider started in lazygit, so that we offer to
+				// continue it once its conflicts are resolved.
+				self.mergeAndRebaseHelper.RecordWhetherMergeOrRebaseStartedInLazygit()
 				return self.mergeAndRebaseHelper.CheckForConflicts(err)
 			}
 
diff --git a/pkg/gui/types/common.go b/pkg/gui/types/common.go
index b81fb15e1..7621f8686 100644
--- a/pkg/gui/types/common.go
+++ b/pkg/gui/types/common.go
@@ -401,6 +401,8 @@ type IRepoStateAccessor interface {
 	GetSearchState() *SearchState
 	SetSplitMainPanel(bool)
 	GetSplitMainPanel() bool
+	GetMergeOrRebaseStartedInLazygit() bool
+	SetMergeOrRebaseStartedInLazygit(bool)
 }
 
 // startup stages so we don't need to load everything at once
diff --git a/pkg/integration/components/common.go b/pkg/integration/components/common.go
index 2d62e9ea3..f338be52f 100644
--- a/pkg/integration/components/common.go
+++ b/pkg/integration/components/common.go
@@ -38,6 +38,14 @@ func (self *Common) AbortMerge() {
 		Confirm()
 }
 
+// PretendMergeOrRebaseStartedInLazygit tells lazygit to treat the in-progress
+// rebase/merge/etc. as one that it started, so that it will prompt to continue
+// once the conflicts are resolved. Use it when a test sets up an operation by
+// running git directly rather than through lazygit's UI.
+func (self *Common) PretendMergeOrRebaseStartedInLazygit() {
+	self.t.gui.PretendMergeOrRebaseStartedInLazygit()
+}
+
 func (self *Common) AcknowledgeConflicts() {
 	self.t.ExpectPopup().Menu().
 		Title(Equals("Conflicts!")).
diff --git a/pkg/integration/components/test_test.go b/pkg/integration/components/test_test.go
index e7d03ada9..e7fd0b66a 100644
--- a/pkg/integration/components/test_test.go
+++ b/pkg/integration/components/test_test.go
@@ -93,6 +93,8 @@ func (self *fakeGuiDriver) CheckAllToastsAcknowledged() {}
 
 func (self *fakeGuiDriver) Headless() bool { return false }
 
+func (self *fakeGuiDriver) PretendMergeOrRebaseStartedInLazygit() {}
+
 func TestManualFailure(t *testing.T) {
 	test := NewIntegrationTest(NewIntegrationTestArgs{
 		Description: unitTestDescription,
diff --git a/pkg/integration/tests/conflicts/merge_file_both.go b/pkg/integration/tests/conflicts/merge_file_both.go
index 083572125..eb1d0b192 100644
--- a/pkg/integration/tests/conflicts/merge_file_both.go
+++ b/pkg/integration/tests/conflicts/merge_file_both.go
@@ -55,6 +55,8 @@ var MergeFileBoth = NewIntegrationTest(NewIntegrationTestArgs{
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
 		_, _, _, expected := testDataBoth()
 
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/merge_file_current.go b/pkg/integration/tests/conflicts/merge_file_current.go
index b80917446..68cf990e5 100644
--- a/pkg/integration/tests/conflicts/merge_file_current.go
+++ b/pkg/integration/tests/conflicts/merge_file_current.go
@@ -54,6 +54,8 @@ var MergeFileCurrent = NewIntegrationTest(NewIntegrationTestArgs{
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
 		_, _, _, expected := testDataCurrent()
 
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/merge_file_incoming.go b/pkg/integration/tests/conflicts/merge_file_incoming.go
index 8216b4a4d..17667b296 100644
--- a/pkg/integration/tests/conflicts/merge_file_incoming.go
+++ b/pkg/integration/tests/conflicts/merge_file_incoming.go
@@ -54,6 +54,8 @@ var MergeFileIncoming = NewIntegrationTest(NewIntegrationTestArgs{
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
 		_, _, _, expected := testDataIncoming()
 
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/pick_both_hunks_diff3.go b/pkg/integration/tests/conflicts/pick_both_hunks_diff3.go
index 59a634c3b..6e9a6eb92 100644
--- a/pkg/integration/tests/conflicts/pick_both_hunks_diff3.go
+++ b/pkg/integration/tests/conflicts/pick_both_hunks_diff3.go
@@ -16,6 +16,8 @@ var PickBothHunksDiff3 = NewIntegrationTest(NewIntegrationTestArgs{
 		shared.CreateMergeConflictFile(shell)
 	},
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/resolve_externally.go b/pkg/integration/tests/conflicts/resolve_externally.go
index ab045f233..bffb2d023 100644
--- a/pkg/integration/tests/conflicts/resolve_externally.go
+++ b/pkg/integration/tests/conflicts/resolve_externally.go
@@ -15,6 +15,8 @@ var ResolveExternally = NewIntegrationTest(NewIntegrationTestArgs{
 		shared.CreateMergeConflictFile(shell)
 	},
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/resolve_externally_started_merge_no_prompt.go b/pkg/integration/tests/conflicts/resolve_externally_started_merge_no_prompt.go
new file mode 100644
index 000000000..ec83f3f08
--- /dev/null
+++ b/pkg/integration/tests/conflicts/resolve_externally_started_merge_no_prompt.go
@@ -0,0 +1,41 @@
+package conflicts
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+	"github.com/jesseduffield/lazygit/pkg/integration/tests/shared"
+)
+
+var ResolveExternallyStartedMergeNoPrompt = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "When a merge started outside lazygit has its conflicts resolved, don't prompt to continue it",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		// Start the merge by running git directly and never tell lazygit it was
+		// the one to start it, so from lazygit's point of view it was started
+		// externally (e.g. by a coding agent in another terminal).
+		shared.CreateMergeConflictFile(shell)
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Contains("UU file").IsSelected(),
+			).
+			Tap(func() {
+				t.Shell().UpdateFile("file", "resolved content")
+			}).
+			Press(keys.Universal.Refresh)
+
+		// No prompt to continue the merge appears; we stay in the files view
+		// with the conflict resolved and the merge still in progress.
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Contains("M  file"),
+			)
+
+		t.Views().Information().Content(Contains("Merging"))
+	},
+})
diff --git a/pkg/integration/tests/conflicts/resolve_multiple_files.go b/pkg/integration/tests/conflicts/resolve_multiple_files.go
index 7dd88e02c..5a8f9447e 100644
--- a/pkg/integration/tests/conflicts/resolve_multiple_files.go
+++ b/pkg/integration/tests/conflicts/resolve_multiple_files.go
@@ -15,6 +15,8 @@ var ResolveMultipleFiles = NewIntegrationTest(NewIntegrationTestArgs{
 		shared.CreateMergeConflictFiles(shell)
 	},
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/conflicts/resolve_without_trailing_lf.go b/pkg/integration/tests/conflicts/resolve_without_trailing_lf.go
index 3deafb288..30ae73e54 100644
--- a/pkg/integration/tests/conflicts/resolve_without_trailing_lf.go
+++ b/pkg/integration/tests/conflicts/resolve_without_trailing_lf.go
@@ -24,6 +24,8 @@ var ResolveWithoutTrailingLf = NewIntegrationTest(NewIntegrationTestArgs{
 			RunCommandExpectError([]string{"git", "merge", "--no-edit", "branch2"})
 	},
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/file/discard_all_dir_changes.go b/pkg/integration/tests/file/discard_all_dir_changes.go
index 6caa3d519..d4c7c4d0f 100644
--- a/pkg/integration/tests/file/discard_all_dir_changes.go
+++ b/pkg/integration/tests/file/discard_all_dir_changes.go
@@ -73,6 +73,8 @@ var DiscardAllDirChanges = NewIntegrationTest(NewIntegrationTestArgs{
 		shell.RunShellCommand(`echo "renamed\nhaha" > dir/renamed2.txt && git add dir/renamed2.txt`)
 	},
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/file/discard_various_changes.go b/pkg/integration/tests/file/discard_various_changes.go
index bc68fd218..453c8708c 100644
--- a/pkg/integration/tests/file/discard_various_changes.go
+++ b/pkg/integration/tests/file/discard_various_changes.go
@@ -16,6 +16,8 @@ var DiscardVariousChanges = NewIntegrationTest(NewIntegrationTestArgs{
 	},
 
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		type statusFile struct {
 			status string
 			label  string
diff --git a/pkg/integration/tests/file/discard_various_changes_range_select.go b/pkg/integration/tests/file/discard_various_changes_range_select.go
index 937c50114..16ecedd04 100644
--- a/pkg/integration/tests/file/discard_various_changes_range_select.go
+++ b/pkg/integration/tests/file/discard_various_changes_range_select.go
@@ -16,6 +16,8 @@ var DiscardVariousChangesRangeSelect = NewIntegrationTest(NewIntegrationTestArgs
 	},
 
 	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Common().PretendMergeOrRebaseStartedInLazygit()
+
 		t.Views().Files().
 			IsFocused().
 			Lines(
diff --git a/pkg/integration/tests/test_list.go b/pkg/integration/tests/test_list.go
index a6105c646..554dc726f 100644
--- a/pkg/integration/tests/test_list.go
+++ b/pkg/integration/tests/test_list.go
@@ -169,6 +169,7 @@ var tests = []*components.IntegrationTest{
 	conflicts.MergeFileIncoming,
 	conflicts.PickBothHunksDiff3,
 	conflicts.ResolveExternally,
+	conflicts.ResolveExternallyStartedMergeNoPrompt,
 	conflicts.ResolveMultipleFiles,
 	conflicts.ResolveNoAutoStage,
 	conflicts.ResolveNonTextualConflicts,
diff --git a/pkg/integration/types/types.go b/pkg/integration/types/types.go
index cd6102cdf..34ce499cc 100644
--- a/pkg/integration/types/types.go
+++ b/pkg/integration/types/types.go
@@ -52,4 +52,9 @@ type GuiDriver interface {
 	NextToast() *string
 	CheckAllToastsAcknowledged()
 	Headless() bool
+	// Record that the in-progress rebase/merge/etc. is to be treated as one
+	// that was started from within lazygit. Lets a test that starts an
+	// operation by running git directly (rather than through the UI) still get
+	// the "continue?" prompt when its conflicts are resolved.
+	PretendMergeOrRebaseStartedInLazygit()
 }