diff --git a/builtin/rebase--interactive.c b/builtin/rebase--interactive.c
index 4535523bf5..d1a4ac1b84 100644
--- a/builtin/rebase--interactive.c
+++ b/builtin/rebase--interactive.c
@@ -171,7 +171,7 @@ static int do_interactive_rebase(struct replay_opts *opts, unsigned flags,
 	struct argv_array make_script_args = ARGV_ARRAY_INIT;
 	struct todo_list todo_list = TODO_LIST_INIT;
 
-	if (prepare_branch_to_be_rebased(opts, switch_to))
+	if (prepare_branch_to_be_rebased(the_repository, opts, switch_to))
 		return -1;
 
 	if (get_revision_ranges(upstream, onto, &head_hash,
diff --git a/sequencer.c b/sequencer.c
index 281a8ade19..ccc0160800 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -3418,10 +3418,11 @@ static const char *reflog_message(struct replay_opts *opts,
 	return buf.buf;
 }
 
-static int run_git_checkout(struct replay_opts *opts, const char *commit,
-			    const char *action)
+static int run_git_checkout(struct repository *r, struct replay_opts *opts,
+			    const char *commit, const char *action)
 {
 	struct child_process cmd = CHILD_PROCESS_INIT;
+	int ret;
 
 	cmd.git_cmd = 1;
 
@@ -3430,25 +3431,31 @@ static int run_git_checkout(struct replay_opts *opts, const char *commit,
 	argv_array_pushf(&cmd.env_array, GIT_REFLOG_ACTION "=%s", action);
 
 	if (opts->verbose)
-		return run_command(&cmd);
+		ret = run_command(&cmd);
 	else
-		return run_command_silent_on_success(&cmd);
+		ret = run_command_silent_on_success(&cmd);
+
+	if (!ret)
+		discard_index(r->index);
+
+	return ret;
 }
 
-int prepare_branch_to_be_rebased(struct replay_opts *opts, const char *commit)
+int prepare_branch_to_be_rebased(struct repository *r, struct replay_opts *opts,
+				 const char *commit)
 {
 	const char *action;
 
 	if (commit && *commit) {
 		action = reflog_message(opts, "start", "checkout %s", commit);
-		if (run_git_checkout(opts, commit, action))
+		if (run_git_checkout(r, opts, commit, action))
 			return error(_("could not checkout %s"), commit);
 	}
 
 	return 0;
 }
 
-static int checkout_onto(struct replay_opts *opts,
+static int checkout_onto(struct repository *r, struct replay_opts *opts,
 			 const char *onto_name, const char *onto,
 			 const char *orig_head)
 {
@@ -3458,7 +3465,7 @@ static int checkout_onto(struct replay_opts *opts,
 	if (get_oid(orig_head, &oid))
 		return error(_("%s: not a valid OID"), orig_head);
 
-	if (run_git_checkout(opts, onto, action)) {
+	if (run_git_checkout(r, opts, onto, action)) {
 		apply_autostash(opts);
 		sequencer_remove_state(opts);
 		return error(_("could not detach HEAD"));
@@ -4786,7 +4793,7 @@ int complete_action(struct repository *r, struct replay_opts *opts, unsigned fla
 	if (todo_list_parse_insn_buffer(r, new_todo.buf.buf, &new_todo) ||
 	    todo_list_check(todo_list, &new_todo)) {
 		fprintf(stderr, _(edit_todo_list_advice));
-		checkout_onto(opts, onto_name, onto, orig_head);
+		checkout_onto(r, opts, onto_name, onto, orig_head);
 		todo_list_release(&new_todo);
 
 		return -1;
@@ -4805,7 +4812,7 @@ int complete_action(struct repository *r, struct replay_opts *opts, unsigned fla
 
 	todo_list_release(&new_todo);
 
-	if (checkout_onto(opts, onto_name, oid_to_hex(&oid), orig_head))
+	if (checkout_onto(r, opts, onto_name, oid_to_hex(&oid), orig_head))
 		return -1;
 
 	if (require_clean_work_tree(r, "rebase", "", 1, 1))
diff --git a/sequencer.h b/sequencer.h
index a515ee4457..6c55aa4200 100644
--- a/sequencer.h
+++ b/sequencer.h
@@ -175,7 +175,8 @@ void commit_post_rewrite(struct repository *r,
 			 const struct commit *current_head,
 			 const struct object_id *new_head);
 
-int prepare_branch_to_be_rebased(struct replay_opts *opts, const char *commit);
+int prepare_branch_to_be_rebased(struct repository *r, struct replay_opts *opts,
+				 const char *commit);
 
 #define SUMMARY_INITIAL_COMMIT   (1 << 0)
 #define SUMMARY_SHOW_AUTHOR_DATE (1 << 1)