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 the club, having a rejected a move from an English club in the past week. A week later, on 22 May 2012, Shiels signed a two-year contract extension. At the start of the 2012–13 season, Shiels was given two-match touchline ban by the SFA in June, having served one suspension on the last game of the season and miss one match at the opening game of the season. His touchline ban was given over commenting made about a referee's decisions made in a match between Celtic and St Johnstone. Following a controversial penalty in a 2-0 defeat against Hibernian on