During the 2009 season, Prado stepped in as the Braves' starter at second base when Kelly Johnson went on the disabled list midway through the season. Prado took full advantage of the opportunity, to the extent that he remained the starter at second, batting second in the lineup, even after Johnson's return to the active roster. Prado's final stats for the season consisted of a .307 average, 14 home runs, 49 RBIs, and 64 runs scored in 450 at-bats over the course of 128 games. In addition to playing 63 games at second, he showed versatility by playing 41 games at third and 28 at first.