When the club finished 11th in Division One in 2000, it was relegated to Division Two North West, finishing 4th in 2001. Striker Dale White finished up as the league’s Top Goalscorer that season with 21 goals. Moved back to it’s traditional South-side home in regionalised leagues, the team took 4th place in Division Two South East. Under coach Andy O’Dell, boosted with Helmut Kalitzki returning as President, the club returned to the First Division by capturing the Division Two South East Championship in 2003. Peter Psarros claimed the Top Goalscorer title for the division, and the reserve team also took out it’s Championship to complete the most successful season in over a decade.

The return to Division One saw the club near the top of the table most of the season, finally finishing in fourth place. New signing Joey Di Iorio shared the League Best and Fairest Award, as well as finishing the division’s top goalscorer. Mid-season acquisition Cameron Jones won the Best and Fairest from another new player in 2004, James Baskerville.

After a patchy start to the 2005 season, Dean Hennessey took over as senior coach after the resignation of Andy O’Dell. English goalkeeper Matt Conkie, defenders Jason Dimozantos and John Petridis, midfielders Craig Kerr, Andy Ross, Craig Murphy and Irish striker Fergal O’Colmain were amongst the new faces that steered the side up the table. Eight unbeaten games through June and July, with the addition to the squad of Xhezair Sulemani, had the side in line for promotion. Winning the last four games of the season saw the club promoted to the Victorian Premier League as runner’s-up behind Kingston City in State League Division One.

It was third time lucky for the club in the top flight, finally managing to survive a season in Victoria’s highest level. After a promising opening round win over Essendon Royals, good results were hard to come by, despite the side playing some good football and creating plenty of chances. Phil Stubbins took over as coach at the end of may, and after two draws the side went on a five game winning streak which lifted it from bottom of the table into the Top Six. In the end the club finished eighth, a win in the final round against Bulleen Zebras not enough to get them back into the Top Six after a loss at Preston Lions the week before.
Youngster Daniel Visevic was named the Best Under 21 Player in the League, and English import James Robinson was recruited by Melbourne Victory of the A-League.

Phil Stubbins led the club into the 2007 VPL season, with Solomon Islands internation Henry Fa’arodo added to the squad. A 4-1 win over Oakleigh Cannons in the last week of April saw the club hit the top of the ladder for a week. The next month Stubbins left to take up the assistant coach position at Adelaide United in the A-League, and was replaced by Doug Hodgson. A mid to late season slump saw a slide down the ladder, with five successive losses seeing a drop into the relagation zone. A 1-0 win over Altona Magic in the penultimate round left the club’s destiny in its own hands in the final week. Needing a draw to ensure top flight survival, the side resoundingly beat Sunshine George Cross 7-0 at Kevin Bartlett Reserve to wind up 10th on the table.

Michael Chatzitrifonos was lured from Western Suburbs to coach the club in 2008, and the loss of Steve Burton and Graham Hockless was covered with the signings of former Socceroo Pablo Cardozo, former All White Aaran Lines and former youth international Richie Cardozo. Future club mainstays Dimitri Tsiaras and Michael Catalano were also signed along with National League players Antun Kovacic and Gerge Goutzioulis. Pablo Cardozo enjoyed a career revival, scoring a hat-trick on debut in a -1 win over Preston Lions en route to becoming the league’s leading scorer and winning the prestigious Bill Fleming Medal for the media’s player of the year. The side finished the season in 5th place, earning a first appearance in the VPL Finals series where it was defeated 1-2 by Heidelberg United in the Elimination Final. The major lowlight of the season was the broken leg suffered by rising star Semir Sivic in his 50th senior appearance for the club in the home game against Heidelberg United in July.

After a promising start, winning four of the first five games, the 2009 season soon unravelled. With Pablo Cardozo moving to Green Gully goalscoring became less free-flowing, and the club would eventually finish just one place above the relegation zone, albeit 14 points clear of the doomed Whittlesea Zebras. New signings included defenders Erhan Karahan and Tom Milardovic and the return in goal of Peter Zois. Young players brought into the squad in the latter half of the season included Enes Sivic, Peter Sawan, Nemanja Govedarica, Stuart Wilson, Mate Eterovic and Tom Uskok. Daniel Visevic returned to the club after spells at Melbourne Knights and in Croatia, but had his season cut short by injury.