In July 2008, Roberto Di Matteo was appointed as the new manager of the Milton Keynes Dons new manager after Paul Ince left to become Blackburn Rovers boss, and Mafe was appointed fitness coach at MK Dons to work alongside Di Matteo and his assistant Eddie Newton.
He followed Paul Ince to Blackburn Rovers soon after and has coached some of England's top players in recent times including Matthew Le Tissier and Paul Gascoigne.
When John Schofield and John Deehan were sacked by Lincoln City on 15 October 2007 following a disappointing start to the 2007–08 season culminating in a 4–0 defeat away to Paul Ince's league leaders, Milton Keynes Dons, Brown was appointed caretaker manager until the appointment of Peter Jackson.
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John stayed on as assistant manager and, with the arrival of Paul Ince moved to Youth Team manager where he was influential in the arrivals of Shaun Brisley, Matthew Flynn, Kristian Dennis and John Rooney into the first-team squad.