Bradley named Muldoon as Connacht captain ahead of the 2008–09 season, replacing Andrew Farley in the role. He led the team out in a competitive game for the first time against the Ospreys on 5 September 2008, but was yellow carded in the match, as the team lost by 3–16. He played in 15 more league games that year, and was sin binned in two more games as Connacht finished bottom of the Celtic League again. Muldoon's first European game as captain came against French side Dax in the 2008–09 European Challenge Cup, and he scored a try as Connacht won by 30 points to 12 away from home. In Muldoon's first season as captain, the team made it past the group stages, but were beaten in the quarter-finals by Northampton Saints.