Bailey initially joined the Cub system in 2006 as its roving minor league
catching instructor, before assuming the managerial reins of the
Daytona Cubs of the Class A
Florida State League in the middle of that season. He then spent 2007 and 2008 as a manager in high classification leagues, including one year as manager of the Smokies. Bailey spent 2007 as pilot of the
Iowa Cubs of the
Triple-A Pacific Coast League, and finished second overall in the PCL American North Division standings with a 79–65 record. In 2008, his Smokies finished in last place in the SL's North Division with a mark of 62–77 (.446). He was replaced by
Ryne Sandberg as Smokies' manager on December 17, 2008. Bailey then returned to Daytona for the 2009–11 seasons. His 2011 Daytona Cubs finished 76–61 during the regular season and won the first-half championship of the Florida State League's Northern Division. The Cubs then won the FSL playoff championship, earning Bailey a promotion to his second term as manager of the Double-A Smokies for 2012. His 2012 club missed the SL playoffs (compiling a record of 72–68), but the 2013 edition finished 76–62, the best overall record in the Southern League North Division, to qualify for the postseason. The Smokies then fell to the eventual league champion
Birmingham Barons in the first playoff round, three games to two. His 2016 Pelicans won 82 of 139 games played (.590) during the regular Carolina League season, then defeated the
Salem Red Sox and
Lynchburg Hillcats in the playoffs to win the league title. Bailey was rehired for the season on December 16, 2016. In , his Pelicans finished 73–67 and won their first-half division title, but fell in the first playoff round. Bailey was invited to return for and his third straight campaign with Myrtle Beach on January 18, 2018. After spending the 2019 season with the Low-A South Bend Cubs, Bailey returned to managing the Pelicans for the 2021 season. He remained the club's manager through the 2024 season making 2 more playoff appearances. He was replaced by Yovanny Cuevas for the 2025 season. ==Death==