But he dramatically walked out on them in November blaming the amateurish way the club dealt with its top players and fears for his family's safety.
He is a bit like an Iranian Jose Mourinho - good looking, with modern methods and a winning touch. His fans know him as the Red Emperor.
He spent his youth in America, learned his craft alongside managers like Dick Advocaat and Guus Hiddink coaching the Korean national team, and then returned to Iran.
"I became a symbol of Iranians living abroad, millions of them, and that gave me an incredible inspiration to create a revolution in football," Ghotbi told the BBC Persian service in an exclusive interview.
And the fans loved it. Ghotbi's team had 30 million fans and crowds of 100,000 would pack into stadiums - where women incidentally are not allowed.
For Iranian football players conditions can be dreadful. Clubs are rich and the players well paid but Ghotbi says they used to lack basic equipment.
Ghotbi tells of players having to shower off using a water hose after training, seldom being able to find socks to wear, pitches with dreadful slopes so that once a ball was kicked "it just kept rolling". Sometimes, the team did not get more than one shirt between them.
"At Persepolis the expectations are enormous it's almost like Chelsea or Manchester United, but the facilities and the organisation around the club is almost worse than a youth amateur club in Europe." says Ghotbi.
'Fragile security'
Ghotbi is now living in Dubai - he's popular with the thousands of other expatriate Iranians who live there in spite of walking out on Persepolis after a series of difficulties with the people who controlled the club.
He and his Korean partner eventually left the country shortly after her car was surrounded by 50 hostile fans armed with stones and sticks.
"It was almost impossible to trust anyone, many things including security seemed a little bit fragile, and I sometimes feel I became too popular for my own good. So with one hand tied and a leg cut off I decided it was almost impossible to succeed."
Ghotbi says the state tries to control a sport loved by millions.
"I suspect that because football controls people's hearts there is a lot of influence from above."
He's now looking for a new footballing challenge - most probably outside Iran.
See this video :
http://212.58.251.203/persian/sport/2009/03/090309_pm_afshin_ghotbi.shtml