The club managed to stay in the Cymru Alliance for a few seasons, but the 2005–06 season proved too much of a challenge for them, and they finished bottom of the table. This ensured the club would be relegated, and would play their football in the Welsh Alliance for the 2006–07 season. Promotion to the Cymru Alliance meant 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 rooms and the showers. More changes are in the pipeline as Halkyn strive to continue building the football club.
