Having begun his career with his home-town side, Wotton went on to become the club's most successful captain as they won two Football League titles in three seasons.

By the time he left Plymouth in 2008, Wotton had broken into the top ten of the club's all-time appearance list – playing in more than 400 matches – and won their Player of the Year award twice.

[5] Renowned for his leadership and powerful shot, Wotton played at both centre half and defensive midfield and was considered a specialist at set pieces.

In the summer of 2006, he was involved in an incident with young striker Chris Zebroski during a pre-season tour of Austria,[10] which required Wotton to have more than a hundred stitches in his head.

[13][14] In his first start he came up against former club Plymouth's archrivals, Exeter City, in the first round of a League Cup match that Southampton comfortably won 3–1.

[15] In March of the 2009-10 season, Wotton got his first taste of silverware away from Argyle, when he played in central midfield for 85 minutes of the 2010 Football League Trophy Final, winning 4–1 against Carlisle United.

[18] On 1 January 2011, Wotton made his debut for Yeovil away in a 0–0 draw to his old side Plymouth, for whom he played for 13 years clocking up nearly 400 appearances, and he received a standing ovation from the Argyle fans when his name was called out on the PA system.

[28] At the end of the 2013–14 season, Wotton signed a new one-year contract to become a player-coach at Home Park replacing Gary Owers who had left the club.

Wotton became a main-stay as a staff member under Adams, and for the 2017-18 season took on management duties for Argyle's Central League South team.

[32] On 28 April 2019, Wotton and Adams were both sacked by Argyle with the club in the League One relegation zone with one game left of the season, following a 5–1 defeat at Accrington Stanley.

[34] On 4 July 2019, it was announced that Wotton had agreed to become the manager of Truro City of the Southern League Premier Division South.

[36] On 14 May 2024, Wotton was appointed manager of fellow National League South side Torquay United on an initial three-year contract, officially taking the post once the Bryn Consortium confirmed their takeover.