On June 12, 2005, Boyer was called up to the major leagues directly from the AA Mississippi Braves, and made his debut that day against the Oakland Athletics. He went 4–1 with a 2.05 ERA in 23 games at Atlanta's home field, Turner Field. In Boyer's first season, playing for the Atlanta Braves as a midseason call-up, he went 4–2 with a 3.11 ERA in 37.2 innings. The following two seasons, he spent the majority of the time in the minors, collecting just 7 appearances total.