The PDL expanded by a further eight franchises in 2000, and the Chicago Sockers won their second straight title, beating the Mid-Michigan Bucks in a close 1-0 Championship game. The single goal was scored by Rodrigo Costa who, having received a pass from teammate Hamid Mehreioskouei, chipped Bucks goalkeeper Eric Pogue from 18 yards through a crowded penaltty area. Fernando Salazar of the Los Angeles-based San Fernando Valley Heroes was the league's MVP, while his teammate Arshak Abyanli took the honors as top goalscorer.
The league grew from 41 to 44 teams in 2001 through the usual mix of relegation from D3Pro, teams folding and new franchises being added. In the semifinals, the Westchester Flames defeated Sioux Falls Spitfire 5-1 and Calgary Storm defeated Des Moines Menace 2-1; in the final, Westchester defeated Calgary 3-1 to take their first league title. Des Moines and Chicago Fire Reserves dominated the 2002 regular season, but both teams stuttered in the playoffs; the PDL final saw the Cape Cod Crusaders defeating the Boulder Rapids Reserve 2-1 to bring the title to the Northeast for the second year in a row. 2002 also saw the debut of the soon-to-be PDL legend, Tomas Boltnar of Des Moines Menace, who secured an unprecedented triple-crown of PDL MVP, Top Scorer and Rookie of the Year.
The mid-2000s was a period of steady growth and consolidation for the PDL. A TV agreement with Fox Soccer Channel saw the PDL Championship game being broadcast live on national television in North America for the first time, and professional teams began investing in the league by adding U-23 development sides as an addition to their senior rosters. Cape Cod repeated as PDL champs in 2003, beating the Chicago Fire Reserves in the final (and despite the presence of Jürgen Klinsmann playing for Orange County Blue Star), while 2004 saw the title head to Florida for the first time as the Central Florida Kraze overcame perennial bridesmaids Boulder Rapids Reserve.
Des Moines Menace took the PDL Championship trophy back to Iowa in 2005 after beating the El Paso Patriots 6-5 on penalty kicks, following a 0-0 draw in the PDL Championship game. 2006 saw the beginning of two seasons of dominance for two teams: the Michigan Bucks and the Laredo Heat. Both teams made the PDL Final in 2006 and 2007, with the Bucks emerging victorious in '06 with a 2-1 win thanks to goals by Kenny Uzoigwe and Ty Shipalane, only for Laredo to get their revenge the following year with an epic penalty kicks win after a 0-0 tie in regulation time.
Laredo became the first team to make three consecutive PDL championship games in 2008, but fell at the final hurdle to Thunder Bay Chill, who became the first ever Canadian side to win the PDL following their 4-1 penalty shootout victory. The PDL had grown to 68 teams by 2009, and to reflect their growing reputation, introduced a new scheme called PDL-Pro, whereby certain teams would be allowed to act as professional clubs, paying players, while still adhering to NCAA collegiate eligibility rules, and the USL's own age restriction policy. Ventura County Fusion returned the PDL title to Southern California for the first time in over a decade with a stoppage-time victory over Chicago Fire Premier, and in doing so became the lowest-seeded team to claim the national title.