While still playing, he became a youth coach at NEC Nijmegen. A keen admirer of the training methods of Wiel Coerver, he went to Qatar at age 29 to work with Coerver, and the national youth players of Qatar. He went on to coach both the Qatar national team under 16's and under 17's youth sides. In 1999, he became manager of Qatari side Al-Etehad (now known as Al-Gharrafa). While Manchester United were lifting the 1999 UEFA Champions League trophy, Meulensteen was lifting the Middle East equivalent Arab Cup trophy. In 2000 he moved to league rivals Al-Sadd, where he managed the team to winning the domestic Emir Cup competition.

As Meulensteen objected to the team management's inclusion of particular foreign players in Al-Saad, he left the club. Having already showed interest in Meulensteen before he moved to Al-Saad, Sir Alex Ferguson and academy director Les Kershaw persuaded him to join Manchester United as "Skills Development Coach" in 2001, coaching all of the youngsters from age 9 to 21. In December 2005, Sir Alex Ferguson promoted him to manage Manchester United's reserve team, after the departure of Ricky Sbragia who left to become first team coach with Sam Allardyce and Sammy Lee at Bolton Wanderers. Meulensteen retained his role as "Skills Development Coach".

In June 2006, he signed a three year contract with Danish club Brøndby IF to become first team coach of the club. Also in 2006, Meulensteen completed his UEFA Pro License. His first half year as Brøndby coach turned out unsuccessful. In the winter break following the first half of the 2006-07 Danish Superliga season, Brøndby were in 7th place, 19 points adrift the leading side, local rivals F.C. Copenhagen. As Brøndby had finished as either champions or runners-up every year since the 1994-95 season, on January 5, 2007, Meulensteen and Brøndby IF dissolved their cooperation. Meulensteen didn't share the same views in the way forward as members of the Brøndby IF board. Meulensteen returned to live in Manchester, while Brøndby IF hired former head coach and then youth trainer Tom Køhlert as head coach for 2½ years.

On 18 January 2007, Meulensteen rejoined Manchester United as technical skills development coach mainly to work with the first team. After the departure in July 2008 of their assistant manager, Carlos Queiroz to Portugal as their national team manager, Meulensteen took over as first team coach, with Mike Phelan being promoted to assistant manager. Both assumed their new roles on 13 August 2008.


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