Having initially been linked with Southampton in 2005, Wotte joined the club as part of the new management team in 2008, with particular responsibility for the development of Southampton's youth squad. He was appointed manager on 23 January 2009, replacing Jan Poortvliet. Southampton drew 2–2 against Norwich City in his first game in charge.
Wotte signed a one-year and a half contract with Romania's Liga I team Universitatea Craiova on 7 January 2010. After a good run of games and victories against Rapid Bucharest, Vaslui, Poli Iasi, Brasov, Astra Ploiesti with a young and talented team, he was suspended on 10 May 2010 for 30 days, after losing two home games, but was still 4 points clear from relegation.
Wotte returned to Egyptian club Ismaily in June 2010. He coached his first competitive game in 18 July, in a game against Algerian side JS Kabylie in the 2010 CAF Champions League. After the public uproar in Egypt early 2011 causing temporarily postponing of The Egyptian League Wotte stayed until April managing the team before returning to the Netherlands.
Wotte was named as the first Performance Director of the Scottish Football Association (SFA) on 23 June 2011. After observing the Scottish national teams and leagues for a few months, Wotte cited James Forrest as being a rare example of a young player who had impressed him. Wotte left the SFA in October 2014, having implemented most of the recommendations of a review conducted by Henry McLeish.