Embarking on the 2000’s, All Stars Academy, managed by Dave Perry, went on a short run of success becoming just the fourth team in the League’s history to accomplish a three-peat. They won ATL titles from 1999-2001, an era when the league permanently switched to using wood bats for all their games. Switching to wood bats in 2000 saw a significant increase in the speed of games and the influx of more college players. The early 2000’s era also saw the charter of a very successful independent program, Waterford Fordians (now known as Waterford Nationals), happen in 2008. That followed short, but solid tenures by the Lansingburgh Royals (2003-10) and South Troy Dodgers (2005-07). The Dodgers finished second in the League in 2006 with a 16-5 record and lost the League Championship Series.That year was the first season manager Joe Altieri and his Athletics won a League title. They would string together two championships, then after a year losing to Davies AC in the 2008 League Championship Series, the Athletics won four more consecutive ATL crowns for the first “four-peat” in League history (2009-12). Davies AC, who entered the league in the early 1990’s also showed they could collect multiple League crowns during this era. Behind General Manager Tom Yovine, Davies won the Championship Series in 2002, 2003, 2005, 2008, three with Yovine playing a dual role as coach and, then a fourth with Yovine as just the GM. AABC Tournament play became more popular during this era with the League hosting more AABC postseason events which resulted in more teams gearing up to participate in them.

The Athletics won nine AABC Upper New York State Championships under Altieri from 1998-2009, which currently stands as a State record. The League, meanwhile, captured two more AABC State titles (Davies AC in 2003, Senators in 2005) during that time to keep the state crown in the Twilight League for 11 straight years heading into 2011. THE2010’sPriorto the 2010 season, Davies AC left the league due to numerous retirements from players, which yielded way for the Blue Slate Blue hawks franchise to enter the ATL. Behind General Manager Gary Pollard, the team was a small core of former Davies players and was competitive right away with top three finishes in its first three seasons. Meanwhile, the Albany Athletics continued their dominance by winning the League title in 2010 and upsetting downstate powerhouse Long Island Storm to win the AABC North Atlantic Regional Tournament and earn a trip to the AABC World Series in Houston. It was the first World Series berth by an ATL team since the 1989 Apex team.

The A’s finished 5th in the World Series that year. A year later Blue Slate and the A’s were separate by only one game in the final standings and while the Hawks went up two-games-to-none in the Championship Series, the A’s came roaring back and swept the final three towing it—the first time a team has come back from two games down since the 1983 Oppenheim Posta year later, the Lansingburgh Royals and All-stars Academy exited making way for the Albany Thunder, run by propane businessman Robert Nolan Sr., and the Chemenergy Diamond Kings, run by Bill Creighton Sr. who had previously run numerous younger level teams. While both teams struggled in 2011, the League still had a strong product on the field.