Quigley made a slow start to his Bohs career and it was 8 May before he netted his first league for the club when scoring the winner against Sligo Rovers. Despite playing as a forward for most of his career, Pat Fenlon decided to use Mark as a winger and this played a part in a strike rate of only 4 goals in 34 league appearances for the Gypsies. When his contract expired at the end of the 2010 season, Quigley was released by Bohemians.