Twiss remained in the Conference for the 2004–05 season, signing with Morecambe in May 2004, after rejecting a new contract at Chester. Performing well at Christie Park, Ian Rush, now manager of old club Chester, offered Morecambe £50,000 for his return, a bid which was rejected. In March 2005 he was singled out for praise, due to his consistent scoring. Again a solid performer in the 2005–06 season, Morecambe crept into the play-offs, only to be defeated by Hereford United. Twiss scored 11 goals in the 2006–07 season before damaging medial ligaments in February. He did however make it back in time for the play-offs, and was part of the Morecambe side that won the Conference play-off Final 2–1 over Exeter City at Wembley. A long-term contract signed in December 2006 would keep him signed to Morecambe until June 2010. He helped Morecambe to survive in their first season in League Two, as they finished 11th and reached the semi-final of the Football League Trophy. Bury aimed to achieve his signature in July 2008, but did not get far. York City attempted to sign him in August 2008, but this ended as Twiss wanted to stay in the Lancashire area. After gradually falling out of favour he was released by Morecambe in March 2010.
