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.
Having ceased to be a football player, Lemonis pursued coaching in England and, in 1996, became head coach at Asteras Zografou. In 2000, he returned to Olympiacos as an assistant coach and, after the dismissal of Giannis Matzourakis, took over as head coach. Lemonis achieved domestic triumphs at Olympiakos by winning two consecutive championships.