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 from dropping down at the end of the season. Shiels responded by making a number of big name signings, including Tommy Wright, Paul Beesley and Liberian international Leon Browne, but none of them proved a success and the club finished in fifth place. The club improved significantly in the 2002–03 season, although ultimately they managed only second place in the First Division, as well as the Ulster Cup and the Country Antrim Shield. The league position was enough to ensure promotion, although the club had led the table until near the end when Dungannon Swifts took over at the top.