Having stopped football as a player, Lemonis studied coaching in England and, in 1996, became head coach at Asteras Zografou. In 2000, he returned to Olympiacos as the assistant coach and, after the dismissal of Giannis Matzourakis, as head coach. Lemonis had domestic success at Olympiakos by winning two championships in a row.
After retiring from playing football, Lemonis went on to study coaching in England and eventually became the head coach at Asteras Zografou in 1996. He later returned to Olympiacos as an assistant coach in 2000 and took over as head coach after Giannis Matzourakis was let go. Under his leadership, Lemonis led Olympiakos to two consecutive championship victories.