In 2006, Williams became a coach in the Tampa Bay Devil Rays organization at the Class A level, and has been a manager with the Short Season-A Hudson Valley Renegades (2009), Class ABowling Green Hot Rods (2010–12), and Class A Charlotte Stone Crabs (2013). He was named the Midwest League's top managerial prospect of 2012 by Baseball America,[2] and through 2018 had compiled a win–loss record of 695–627 (.526). From 2014–2018, he spent five years as skipper of the Montgomery Biscuits, the Rays' Double-A affiliate.[3] In his second year in Montgomery, Williams led his club to the second-half North Division championship and the Southern League playoffs. He also led the 2016 and 2017 Biscuits to playoff berths. On January 18, 2019, Williams was named the manager of the Durham Bulls.[4] In three full seasons at Durham (interrupted by the 2020 minor-league shutdown due to the COVID-19 pandemic), Williams posted a 247–172 (.589) record, including winning Triple-A national championships in 2021 and 2022, and finishing runner-up in the 2019Governors' Cup playoffs.[5]
On November 14, 2022, Williams was officially announced as the Rays' new third base coach, replacing Rodney Linares.[6]
Brady Williams' younger brother Shawn is a minor league manager and former player; he has been a skipper in the Philadelphia Phillies' farm system since 2014.