Despite reported interest from English clubs Manchester United, Arsenal, and Spanish club Real Madrid, rumors of a move to rivals Olympique de Marseille began to surface. On 28 June 2008, Lyon confirmed that a proposed transfer to Marseille had been canceled for the time being. However, Ben Arfa confirmed to the local La Provence newspaper on 29 June that he had signed for the southern coast club and would not return to Lyon for preseason training the following day on 30 June. La Provence later reported that Ben Arfa had in fact missed training in Lyon that day, confirming his intentions.

Ben Arfa officially joined Marseille on 1 July 2008 for €11 million with future incentives to be included later, after an agreement was reached between Marseille and Lyon in a meeting organized by the LFP. As a result of the conflict over the transfer, in December of 2008, Ben Arfa told the French paper Le Progrès that his former team, Olympique Lyonnais, lacks class and is not a great team. Ben Arfa was presented to the media and had his first training session with the club the same day. He was assigned the number 20 shirt. On 16 July, Ben Arfa was involved in another training session scuffle, this time with stiker and France international Djibril Cissé. Cissé later joined English club Sunderland on loan.

Ben Arfa made his league debut on the opening match day in a thrilling 4–4 draw with Rennes. He scored his first goal for the Marseilles in that match. He continued great form scoring 6 times in his first 11 matches, however, his past would continue to haunt him as he would be involved in another dispute this time with the Cameroon international Modeste M'Bami following the club's UEFA Champions League match with Liverpool. The two had to be separated by Ronald Zubar. Controversy arose again following Marseille embarrassing 2–4 loss to Le Classique rivals Paris-Saint Germain. He drew the ire of manager Eric Gerets after his refusal to leave the bench to warm up. Ben Arfa cited an injury as his reason much to the chagrin of Gerets and later apologized for the incident to the media and Gerets himself.^] Upon his return to the squad, Ben Arfa responded by scoring a goal and providing the assists on both the other goals in a 3–1 victory over Saint-Étienne.