On 20 February 2013, Torquay United appointed Knill as caretaker manager in place of Martin Ling, who had gone on sick leave. Knill's objective was to keep The Gulls in the football league and that was achieved on the final day of the season with a 3–3 draw at home to Bristol Rovers. Knill saw his efforts with Torquay as a success, and felt he had "improved his CV" by helping the club avoid relegation. On 7 May 2013 he was appointed the permanent manager of Torquay. Knill was sacked on 2 January 2014 with the club having won only five league games in the 2013–14 season and sitting 23rd in League Two.