Baseball Hall of Fame inductees Billy Williams, Paul Molitor and Larry Walker played for Burlington.

The Bees play in the Prospect League's Western Conference – Northwest Division along with the Clinton LumberKings, Illinois Valley Pistol Shrimp, and Springfield Lucky Horseshoes.

The franchise then returned as the Burlington Indians in 1947, the same year that their current stadium, Community Field, opened.

The team joined the Three-I (Illinois, Iowa, Indiana) League in 1952 as the Burlington Flints but was renamed the Bees in 1954.

From 1963 through 1974 they were a farm team of the Kansas City (later Oakland) A's; subsequent affiliations included the Brewers (1975–81), Rangers (1982–85), Expos (1986–87 and 1993–94), Braves (1988–90), Astros (1991–92), Giants (1995–96), Reds (1997–98), and White Sox (1999–2000).

In addition to Baseball Hall of Famers Billy Williams, Paul Molitor and Larry Walker, many former Burlington players have enjoyed major league success including: Sal Bando, Vida Blue (who struck out a team-record 231 batters in 1968), George Hendrick, Phil Garner, Chet Lemon, Claudell Washington, Rubén Sierra, Kenny Rogers, José Vidro, Ugueth Urbina, Javy López, Mark Buehrle, Mike Moustakas, and Salvador Pérez.

The stadium was upgraded again prior to the 2004 season, including a revamped concessions area, partial covering of the grandstand, improved sound system, and a new scoreboard.