diff --git a/rebase-interactive.c b/rebase-interactive.c
index 1ff07647af3..7407c593191 100644
--- a/rebase-interactive.c
+++ b/rebase-interactive.c
@@ -146,6 +146,12 @@ int edit_todo_list(struct repository *r, struct todo_list *todo_list,
 		return -4;
 	}
 
+	/*
+	 * See if branches need to be added or removed from the update-refs
+	 * file based on the new todo list.
+	 */
+	todo_list_filter_update_refs(r, new_todo);
+
 	return 0;
 }
 
diff --git a/sequencer.c b/sequencer.c
index ce8c7d8cd3a..67812c0294f 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -4143,6 +4143,102 @@ cleanup:
 	return result;
 }
 
+/*
+ * Parse the update-refs file for the current rebase, then remove the
+ * refs that do not appear in the todo_list (and have not had updated
+ * values stored) and add refs that are in the todo_list but not
+ * represented in the update-refs file.
+ *
+ * If there are changes to the update-refs list, then write the new state
+ * to disk.
+ */
+void todo_list_filter_update_refs(struct repository *r,
+				  struct todo_list *todo_list)
+{
+	int i;
+	int updated = 0;
+	struct string_list update_refs = STRING_LIST_INIT_DUP;
+
+	sequencer_get_update_refs_state(r->gitdir, &update_refs);
+
+	/*
+	 * For each item in the update_refs list, if it has no updated
+	 * value and does not appear in the todo_list, then remove it
+	 * from the update_refs list.
+	 */
+	for (i = 0; i < update_refs.nr; i++) {
+		int j;
+		int found = 0;
+		const char *ref = update_refs.items[i].string;
+		size_t reflen = strlen(ref);
+		struct update_ref_record *rec = update_refs.items[i].util;
+
+		/* OID already stored as updated. */
+		if (!is_null_oid(&rec->after))
+			continue;
+
+		for (j = 0; !found && j < todo_list->total_nr; j++) {
+			struct todo_item *item = &todo_list->items[j];
+			const char *arg = todo_list->buf.buf + item->arg_offset;
+
+			if (item->command != TODO_UPDATE_REF)
+				continue;
+
+			if (item->arg_len != reflen ||
+			    strncmp(arg, ref, reflen))
+				continue;
+
+			found = 1;
+		}
+
+		if (!found) {
+			free(update_refs.items[i].string);
+			free(update_refs.items[i].util);
+
+			update_refs.nr--;
+			MOVE_ARRAY(update_refs.items + i, update_refs.items + i + 1, update_refs.nr - i);
+
+			updated = 1;
+			i--;
+		}
+	}
+
+	/*
+	 * For each todo_item, check if its ref is in the update_refs list.
+	 * If not, then add it as an un-updated ref.
+	 */
+	for (i = 0; i < todo_list->total_nr; i++) {
+		struct todo_item *item = &todo_list->items[i];
+		const char *arg = todo_list->buf.buf + item->arg_offset;
+		int j, found = 0;
+
+		if (item->command != TODO_UPDATE_REF)
+			continue;
+
+		for (j = 0; !found && j < update_refs.nr; j++) {
+			const char *ref = update_refs.items[j].string;
+
+			found = strlen(ref) == item->arg_len &&
+				!strncmp(ref, arg, item->arg_len);
+		}
+
+		if (!found) {
+			struct string_list_item *inserted;
+			struct strbuf argref = STRBUF_INIT;
+
+			strbuf_add(&argref, arg, item->arg_len);
+			inserted = string_list_insert(&update_refs, argref.buf);
+			inserted->util = init_update_ref_record(argref.buf);
+			strbuf_release(&argref);
+			updated = 1;
+		}
+	}
+
+	if (updated)
+		write_update_refs_state(&update_refs);
+	string_list_clear(&update_refs, 1);
+}
+
 static int do_update_ref(struct repository *r, const char *refname)
 {
 	struct string_list_item *item;
diff --git a/sequencer.h b/sequencer.h
index e671d7e0743..98f3bcc1658 100644
--- a/sequencer.h
+++ b/sequencer.h
@@ -132,6 +132,18 @@ void todo_list_release(struct todo_list *todo_list);
 const char *todo_item_get_arg(struct todo_list *todo_list,
 			      struct todo_item *item);
 
+/*
+ * Parse the update-refs file for the current rebase, then remove the
+ * refs that do not appear in the todo_list (and have not had updated
+ * values stored) and add refs that are in the todo_list but not
+ * represented in the update-refs file.
+ *
+ * If there are changes to the update-refs list, then write the new state
+ * to disk.
+ */
+void todo_list_filter_update_refs(struct repository *r,
+				  struct todo_list *todo_list);
+
 /* Call this to setup defaults before parsing command line options */
 void sequencer_init_config(struct replay_opts *opts);
 int sequencer_pick_revisions(struct repository *repo,
diff --git a/t/lib-rebase.sh b/t/lib-rebase.sh
index ec6b9b107da..b57541356bd 100644
--- a/t/lib-rebase.sh
+++ b/t/lib-rebase.sh
@@ -207,3 +207,18 @@ check_reworded_commits () {
 		>reword-log &&
 	test_cmp reword-expected reword-log
 }
+
+# usage: set_replace_editor <file>
+#
+# Replace the todo file with the exact contents of the given file.
+set_replace_editor () {
+	cat >script <<-\EOF &&
+	cat FILENAME >"$1"
+
+	echo 'rebase -i script after editing:'
+	cat "$1"
+	EOF
+
+	sed -e "s/FILENAME/$1/g" <script | write_script fake-editor.sh &&
+	test_set_editor "$(pwd)/fake-editor.sh"
+}
diff --git a/t/t3404-rebase-interactive.sh b/t/t3404-rebase-interactive.sh
index 2fffcf5d5fb..bebf9b4def7 100755
--- a/t/t3404-rebase-interactive.sh
+++ b/t/t3404-rebase-interactive.sh
@@ -1834,6 +1834,145 @@ test_expect_success '--update-refs updates refs correctly' '
 	test_cmp_rev HEAD refs/heads/no-conflict-branch
 '
 
+test_expect_success 'respect user edits to update-ref steps' '
+	git checkout -B update-refs-break no-conflict-branch &&
+	git branch -f base HEAD~4 &&
+	git branch -f first HEAD~3 &&
+	git branch -f second HEAD~3 &&
+	git branch -f third HEAD~1 &&
+	git branch -f unseen base &&
+
+	# First, we will add breaks to the expected todo file
+	cat >fake-todo-1 <<-EOF &&
+	pick $(git rev-parse HEAD~3)
+	break
+	update-ref refs/heads/second
+	update-ref refs/heads/first
+
+	pick $(git rev-parse HEAD~2)
+	pick $(git rev-parse HEAD~1)
+	update-ref refs/heads/third
+
+	pick $(git rev-parse HEAD)
+	update-ref refs/heads/no-conflict-branch
+	EOF
+
+	# Second, we will drop some update-refs commands (and move one)
+	cat >fake-todo-2 <<-EOF &&
+	update-ref refs/heads/second
+
+	pick $(git rev-parse HEAD~2)
+	update-ref refs/heads/third
+	pick $(git rev-parse HEAD~1)
+	break
+
+	pick $(git rev-parse HEAD)
+	EOF
+
+	# Third, we will:
+	# * insert a new one (new-branch),
+	# * re-add an old one (first), and
+	# * add a second instance of a previously-stored one (second)
+	cat >fake-todo-3 <<-EOF &&
+	update-ref refs/heads/unseen
+	update-ref refs/heads/new-branch
+	pick $(git rev-parse HEAD)
+	update-ref refs/heads/first
+	update-ref refs/heads/second
+	EOF
+
+	(
+		set_replace_editor fake-todo-1 &&
+		git rebase -i --update-refs primary &&
+
+		# These branches are currently locked.
+		for b in first second third no-conflict-branch
+		do
+			test_must_fail git branch -f $b base || return 1
+		done &&
+
+		set_replace_editor fake-todo-2 &&
+		git rebase --edit-todo &&
+
+		# These branches are currently locked.
+		for b in second third
+		do
+			test_must_fail git branch -f $b base || return 1
+		done &&
+
+		# These branches are currently unlocked for checkout.
+		for b in first no-conflict-branch
+		do
+			git worktree add wt-$b $b &&
+			git worktree remove wt-$b || return 1
+		done &&
+
+		git rebase --continue &&
+
+		set_replace_editor fake-todo-3 &&
+		git rebase --edit-todo &&
+
+		# These branches are currently locked.
+		for b in second third first unseen
+		do
+			test_must_fail git branch -f $b base || return 1
+		done &&
+
+		# These branches are currently unlocked for checkout.
+		for b in no-conflict-branch
+		do
+			git worktree add wt-$b $b &&
+			git worktree remove wt-$b || return 1
+		done &&
+
+		git rebase --continue
+	) &&
+
+	test_cmp_rev HEAD~2 refs/heads/third &&
+	test_cmp_rev HEAD~1 refs/heads/unseen &&
+	test_cmp_rev HEAD~1 refs/heads/new-branch &&
+	test_cmp_rev HEAD refs/heads/first &&
+	test_cmp_rev HEAD refs/heads/second &&
+	test_cmp_rev HEAD refs/heads/no-conflict-branch
+'
+
+test_expect_success '--update-refs: check failed ref update' '
+	git checkout -B update-refs-error no-conflict-branch &&
+	git branch -f base HEAD~4 &&
+	git branch -f first HEAD~3 &&
+	git branch -f second HEAD~2 &&
+	git branch -f third HEAD~1 &&
+
+	cat >fake-todo <<-EOF &&
+	pick $(git rev-parse HEAD~3)
+	break
+	update-ref refs/heads/first
+
+	pick $(git rev-parse HEAD~2)
+	update-ref refs/heads/second
+
+	pick $(git rev-parse HEAD~1)
+	update-ref refs/heads/third
+
+	pick $(git rev-parse HEAD)
+	update-ref refs/heads/no-conflict-branch
+	EOF
+
+	(
+		set_replace_editor fake-todo &&
+		git rebase -i --update-refs base
+	) &&
+
+	# At this point, the values of first, second, and third are
+	# recorded in the update-refs file. We will force-update the
+	# "second" ref, but "git branch -f" will not work because of
+	# the lock in the update-refs file.
+	git rev-parse third >.git/refs/heads/second &&
+
+	git rebase --continue 2>err &&
+	grep "update_ref failed for ref '\''refs/heads/second'\''" err
+'
+
 # This must be the last test in this file
 test_expect_success '$EDITOR and friends are unchanged' '
 	test_editor_unchanged
