Balotelli's disciplinary problems and difficult relationship with Mourinho continued in the 2009–10 season. In November, Inter drew 1–1 against Roma and Mourinho criticized his players, even going as far as saying that Balotelli "came close to a zero rating". The young striker again incurred the wrath of Juve fans in the heated Derby d'Italia away encounter with Juventus on 5 December 2009 which Inter lost 2–1. When he was elbowed by Juve midfielder Felipe Melo in the shoulder, he fell on the pitch clutching his face and was promptly booked while Melo was sent off for a second yellow card. The incident sparked a fiery altercation between teammate Thiago Motta and Juve goalkeeper Gianluigi Buffon. The falling-out between player and manager reached its peak in the eve of the UEFA Champions League second leg against Chelsea, after the young striker was not called-up following an altercation with Mourinho. The youngster was then criticized by several senior players such as captain Javier Zanetti and veteran defender Marco Materazzi as well as his own agent. in the wake of Inter's 1–0 win at Stamford Bridge, London. In March, he came under heavy criticism from fans after he publicly sported a Milan (Inter's crosstown rivals) jersey on the Italian show Striscia la Notizia.
In the wake of recent tense situation, Balotelli released a statement of apology in Internazionale's official website, that reads:
“ "I am sorry for the situation that has been created recently. I am the first person who has suffered because I adore football and I want to play, and now I am waiting in silence so I can return to being useful to my team. I want to put the past behind me, look to the future and concentrate on the upcoming commitments and make myself ready."
Mario Balotelli
”
After being frozen out of the team due to the situation, Balotelli was recalled to the squad for the match against Bologna and he marked his return with a goal in a 3–0 win. However, he once again caused controversy in a Champions League semi-final against Barcelona on 20 April, as he threw his jersey on the ground after the final whistle, in response to Inter fans who had booed him to criticize his poor performance;his reaction, which caused notable disappointment among fans, teammates and football pundits, was succeeded by an attempt by a small group of supporters to physically attack Balotelli after the end of the game.