After the knee injury, Appleton stayed with West Brom in a coaching capacity. He worked in the club's youth side for five years. He worked with different age groups before moving up to the senior squad as assistant manager. In June 2009, Appleton was appointed first-team coach. After the board sacked Roberto Di Matteo and placed him on gardening leave on 6 February 2011, Appleton was placed in temporary charge of first-team affairs. In his only match in charge, West Brom drew 3–3 at home to West Ham, having been 3–0 up at half-time.
