On 29 May 2008, he was announced as the new Head Coach of English Football League Championship side Southampton as an immediate replacement to Nigel Pearson, with Mark Wotte taking over the Academy. In taking the Southampton job he became the club’s 10th head coach in as many years as well as being the first foreigner to hold the position. But within days it emerged that Poortvliet was still employed by his previous club Helmond Sport who hadn't given him any permission to talk to Southampton. Poortvliet was offering to pay compensation to Helmond where he still had one year on his contract. But his offer of 30,000 Euros was taken as an insult by Helmond. The situation though was resolved via an arbitration panel (The Dutch FA – KNVB). Poortvliet was told he could take the Southampton job if he paid his former club Helmond Sport £60,000 (75,000 euros) in compensation. He complied with these terms and his contract with Helmond Sport was terminated.
In his first official game in charge Southampton lost 2–1 to Cardiff, having conceded right at the end. However, three days later Poortvliet recorded his first win as Southampton manager, beating Exeter City 3–1 in the League Cup first round. His first league win came on 23 August at Derby County thanks to a David McGoldrick goal. Following a run of just one win in 14 home games, on 23 January 2009 Poortvliet announced his resignation from the Club, with reserve team coach Mark Wotte taking over as head coach.
On 15 June 2009, Poortvliet was announced as the new manager of Eerste Divisie club FC Eindhoven. He led his side to qualification to the promotion/relegation tournament between Eredivisie and Eerste Divisie.
On June 2010 he was introduced as new head coach of Telstar, another Dutch Eerste Divisie team; his salary will however be paid by parent club AZ. After two lacklustre seasons at the Velsen-based club, on March 2012 it was confirmed Poortvliet had agreed to a move back to his previous club FC Den Bosch, effective from July.