Berg split his second season in the Twins' organisation, 2006, between the Beloit Snappers batting at a .192/.313/.308 clip, and the Elizabethton Twins, where he hit .253/.353/.466. Over the course of the season, he played every infield position but pitcher and shortstop. He spent the 2007 minor league season with Beloit, struggling again with .214/.298/.291 in 101 games. He played five different positions (1B, 3B, C, RF and LF) in addition to DH.
Berg split the 2008 season between the Fort Myers Miracle (.279/.381/.414 in 67 games) and the New Britain Rock Cats (.255/.327/.319 in 15 games). In 2009, Berg hit just .210 in 60 games between New Britain and Fort Myers, and was designated for assignment. On 24 July, he signed with the Grand Prairie AirHogs of the independent American Association. In 36 games with Grand Prairie, he batted .252 with three home runs and sixteen RBIs.
Australia
In the 2006 Claxton Shield, he went 8 for 18 with a tournament best eleven walks in seven games for the Aces. In the 2007 Claxton Shield, Berg batted .259 for Victoria to help them win the Shield title.
Berg starred in the Claxton Shield 2008, hitting .400/.429/.750 with 3 home runs, second to Olympic Silver Medalist Tom Brice. Daniel was selected for the Australian national baseball team in the 2008 Final Olympic Qualification Tournament and played regularly, batting .308/.367/.462 with seven runs in seven games.