His prolific offensive performances continued through to the opening of the 2008–09 season, despite the club's poor run of form, as he scored 2 goals in the league against Reggina and Atalanta, and 2 more in the UEFA Champions League, against Cluj and Chelsea. On 25 January 2009, Panucci was dropped from Roma's first team squad after refusing to sit on the bench for a league match against Napoli, and was later also excluded from the Champions League squad list. Due to his difficult relationship with manager Luciano Spalletti, he announced his intention to leave Roma, but no serious bidder was found in the January transfer window and he ultimately stayed, returning to the first team on 28 February after he officially apologised to his fellow players and the club management. He was sent off in the second Derby della Capitale of the 2008–09 season after a heated on-pitch clash with Lazio player Stephan Lichtsteiner following his hard challenge on the Swiss defender. His contract with Roma ended on 30 June 2009, which he had signed in October 2005, making him a free agent.