After eight successful seasons as manager of the International League Durham Bulls, the Triple-A affiliate of the Tampa Bay Rays (2007–2014), Montoyo was a candidate for the Rays' 2015 managerial opening and was ultimately brought on as the team's third base coach.
After the 2017 season, he became the Rays’ bench coach.
On October 25, 2018, the Toronto Blue Jays announced that Montoyo had been hired as their new manager.