On 11 July 2006, Beenhakker was appointed as the manager of the Polish national team. Originally, he was appointed to manage Poland until the end of Euro 2008, however, his contract was prolonged until November 2009 and the end of World Cup 2010 qualifiers. On 17 November 2007, beating Belgium 2–0, he managed to qualify with Poland for the European championships – the first coach ever to do so; even in its golden years, the seventies and eighties, Poland never qualified to play in the Euros. On 20 February 2008, he was decorated with the Order of Polonia Restituta by the Polish PresidentLech Kaczyński. The Order can be conferred for outstanding achievements in the fields of education, science, sport, culture, art, economics, defense of the country, social work, civil service, or for furthering good relations between countries.
Upon Poland's failure to qualify for World Cup 2010, Beenhakker was sacked as coach.
While still in charge of Poland, Feyenoord hired him on 5 May 2007 as an interim coach to lead the team through the 2006–07 play-offs. After his departure from Poland, he was named the sports director of the Dutch club, having signed a contract on 9 October 2009 up to 30 June 2011.
Following his spell in the Netherlands, Beenhakker agreed on a three-year deal with Hungarian first division side Újpest FC, and was officially introduced as the new sports director of the purple-whites in a press conference on 29 July 2011. As managing director Csaba Bartha revealed, Beenhakker's main duty is to work with the first team; however, they also intended to use his diverse and extensive personal relationships to establish a scouting network across Europe, which could be used in both directions. His contract was terminated in October 2011, after Belgian businessman Roderick Duchatelet, son of Roland Duchâtelet, bought the club.