Luton went into administration during the 2007–08 season and Coyne was sold to Colchester United for a Colchester record transfer fee of £350,000 in January 2008 to obtain necessary funding for the club. Colchester manager Geraint Williams said: "It's great news for the club. Chris is a defender with experience and leadership qualities." However, Coyne was unable to help prevent Colchester from being relegated at the end of the season. Coyne was named Colchester United club captain for the 2008–09 season, but selection for the Australia national team, injuries and a change of management meant that he struggled to hold on to a place in the first team, and at the end of the season, he met with the club management to resolve his future. He left the club by mutual consent in July 2009, saying, "Unfortunately, after 18 months here, it's time to move on. It was made clear that I wasn't going to play week in, week out and I felt that I had to look at that and address it. Also, there isn't much of a chance for the Australian manager to watch League One football but in Australia, I'm guaranteed to play 27 games in front of him." Coyne scored once for the club, his goal coming in a 4–3 defeat against West Bromwich Albion on 29 March 2008.