When Jeff Kenna resigned, new manager Pete Mahon came in and immediately put Clarke into the team. Clarke played in the final 10 games of the 2009 season and put in some fine performances. He kept 4 clean sheets in the 10 games including clean sheets against the Saints relegation rivals Bray Wanderers twice and Dundalk, and also keeping a clean sheet in the vital last game of the season against Shamrock Rovers.
Following Jeff Kenna's departure, Pete Mahon became manager and quickly added Clarke to the team for the final 10 games of the 2009 season.  Clarke performed well during this period, recording four clean sheets in those ten matches, including shutouts against Bray Wanderers twice and Dundalk, as well as a crucial clean sheet in the last game of the season against Shamrock Rovers.