During the 2002–2003 period he was the assistant coach of
Ivan Jovanovic in Iraklis, as well as the next period, assisting head coach
Sergio Markarián. After Markarián resigned, Kofidis took in charge as the head coach. The next year, with Kofidis taking the reins, was hugely successful as "The Old One", against all expectations, finished 4th in the
2005–2006 Alpha Ethniki championship, and qualified for the
UEFA Cup. During the summer, however, many key players were sold as the team was in heavy debt, and the following year was anything but successful. After a string of 10 league matches without a win, and an early exit from the UEFA Cup against Polish team
Wisła Kraków, Kofidis resigned. In January 2007 he became head coach in
Skoda Xanthi following
Takis Lemonis's resignation, but soon left the job. On 30 October 2009 the club officials of Iraklis have sacked the manager,
Oleg Protasov to replace him with Kofidis. ==Career statistics==