Mortimer quit the Mayo football panel the week of the 2012 Connacht football final against Sligo after losing his place on the first team to Enda Varley. Former manager John Maughan expressed regret that Mortimer still has much to offer the county cause. A Mortimerless Mayo went on to reach the 2012 All-Ireland Senior Football Championship Final, which they lost to Donegal. Conor is the all time leading championship scorer for Mayo.
Mortimer infamously paid to tribute to music icon Michael Jackson shortly after his death in the 2009 Connaught Final. He raised his jersey to reveal a t-shirt with the words 'RIP Micheal Jackson' after scoring Mayo's second goal to earn a one point win. Despite scoring the winning goal Mortimer made national headlines