It is not yet known who will replace him.
Mahaffy will take over from Gary Robinson, who has been acting managing director since David Sloan stood down to be non-executive chairman before Christmas. Robinson was brought in from Vibe FM. The role involves overseeing Downtown Radio and Cool FM. The regional division is undergoing a series of personnel changes.
In January, Emap Radio told staff at Downtown Radio and Cool FM it was making up to 15 full-time positions redundant. The consultation is ongoing. However, it is understood that many of these jobs are technical support and newsroom positions.
Meanwhile, the company is interviewing for the newly created positions of commercial director and agency sales manager.
Trinity Mirror's Northern Irish division sells into the Daily Mirror, the Sunday Mirror and The People.
Earlier this month, the Mirror's website, www.mirror.co.uk, was relaunched with more multimedia elements and a dedicated focus on news, showbiz and sports.
Parent company Trinity Mirror's preliminary financial results are due to be released on 1 March.