Jimmy Nicholl followed Calderwood when he took over as manager at Aberdeen, again serving as his assistant until the two parted company with the club in May 2009. He resumed his partnership with Calderwood at Kilmarnock in 2010. Nicholl was appointed manager of Cowdenbeath in June 2010, but he left Cowdenbeath at the end of the 2010–11 season after they were relegated from the First Division. Nicholl was then appointed assistant manager of Kilmarnock for a second time, by Kenny Shiels on 15 June 2011. Kilmarnock won the 2011–12 Scottish League Cup under Shiels and Nicholl, but Shiels was sacked by Kilmarnock
Kenny Shiels several signings, the club, remained bottom of the league and a 2-0 loss against Alloa Athletic on 12 April 2014 confirmed relegation for Morton. Despite being relegated, it was initially believed that Shiels would stay on as the Greenock Morton boss for the next season, and attempt to return Morton to the Championship, similar to his experience during his time at Coleraine. However, Shiels resigned on May 2014 following a 10-2 defeat by Hamilton Academical which ended a poor season and relegation from the Scottish Championship. Immediately after the match, Shiels said in the post-match press conference, that he was