Muldoon was runner-up for the third time in the Derry Championship in 2003, losing to local rivals An Lúb in the final. He gained his fourth Derry Championship medal in 2006 with the club, avenging the 2003 loss to An Lúb, with Muldoon having an "impressive game". Ballinderry reached the 2006 Ulster Club final, but lost narrowly to Crossmaglen Rangers. In 2008 Muldoon and Ballinderry won the Ulster Senior Club Football League. Muldoon won his fifth Derry Championship medal in 2008, this time as captain. An achilles injury forced him to miss the quarter-final tie with Bellaghy and he was only fit enough to come on as a substitute in the semi-final clash with Dungiven. However he recovered in time for the final, and his performance, particularly in the second half, proved vital in helping the club defeat Slaughtneil. Ballinderry got to the 2008 Ulster Club final and again faced Crossmaglen. Muldoon put in a brilliant performance in the game, which finished a draw. He broke a bone in his foot two days before the replay and could not play. His absence proved costly and Cross won the replay.