Promotion to the Cymru Alliance meant that work was required at Pant Newydd to bring the ground up to the required standard. A makeshift stand was built and changes made to the changing rooms and showers. In the seasons 2000-01 and 2001-02 Halkyn consolidated their position in the Cymru Alliance and once again progressed in the Welsh Cup by eliminating Rhayader Town only to fall to Flexsys Cefn Druids by a narrow 1-0 margin.

In the 2002-03 season George Thelwell took a break from management and the new pairing of Gareth Thomas and Andy Nichols faced a stiff challenge having lost some key players in the close season. Against all the odds the new team finished in their highest place in sixth.
Results in season 2003-04 were good and further consolidated Halkyn’s position in the top half of the table with an eighth place finish and an appearance in the North Wales Coast FA Challenge Cup final. Sadly Rhyl proved too strong on the day.

A tremendous result in the Welsh Cup was achieved in 2004-05 beating Port Talbot of the League of Wales away from home to set alongside a mid-table finish in the Cymru Alliance. Several of the more experienced players retired at the end of the season including Keith Davies and Julian Jones who were stalwarts of the club.

The clubs history since 2004-2005 has been traumatic. Gareth Thomas left the club for a short time to manage Llandudno before returning and then leaving once again for Mynydd Isa. Dave Abraham, picked up the club at a low ebb in the season 2005-06 and despite his considerable efforts, with a depleted squad, could not save the club from a relegation spot.