Although Olympiacos was eventually crowned champion, the loss of the derby of the eternal enemies, the disqualification by a lower division club in the Greek Cup and the loss of Rivaldo led Olympiacos fans to boo Lemonis, Sokratis Kokkalis (the chairman of the club) and the players.

The 2007–08 season started badly with Olympiacos losing points in the Greek Superleague and drawing with Lazio at home.

As coach of Olympiacos, Lemonis has achieved a great amount in both their domestic and UEFA Champions League campaigns.

In his second reign as coach, Lemonis gave Olympiacos their first away win in the competition against SV Werder Bremen, and a trip to the Round of 16 for only the second time in their history in 2007–08.

On 12 November 2008, Lemonis signed a contract for rest of the 2008–09 season and replaced Ewald Lienen as the head coach of Panionios.

[4] Despite being credited with taking the team from fifth place to first in the Superleague table before Christmas, he was relieved of his duties on 4 January 2018, while being offered the opportunity to remain at the club through an alternative staff role;[5] alleged reasons for his dismissal were his difficulties in handling the dressing room and employing well-defined tactical plans,[6] as well as his passive Champions League mentality with an objective of not recording heavy losses rather than being competitive against stronger opposition.