Upon retiring, Ross started as a coaching career at Dumbarton, as assistant manager for both Alan Adamson and later Ian Murray, and was caretaker manager between them. He became the coach of the Heart of Midlothian under-20 team in July 2014. Ross was appointed Alloa Athletic manager in December 2015. In October 2016, he was appointed manager of St Mirren, leading them to the 2017–18 Scottish Championship title and was named PFA Scotland Manager of the Year, before leaving to become manager of Sunderland in May 2018. Ross was sacked by Sunderland in October 2019, and was then appointed by Hibernian a month later.