The Irish international midfielder has just started several months of recovery and recuperation after undergoing an operation for a fractured knee.
It is the latest setback to befall Mahon since he began his second spell with Rovers last summer.
The 32-year-old Dubliner made fewer than 20 first-team appearances last season as injuries and illness hampered his attempts to achieve full match fitness and sharpness.
Now Mahon faces a long haul back from surgery and is unlikely to be ready for League One action until November or December.
Manager Les Parry said: “Alan had a micro-fracture in his knee, a little hole in the surface. He underwent surgery and the hole was drilled so he can’t put any weight on the leg for six to eight weeks.
“It will be getting towards Christmas before he can train and play. It is very unfortunate for him.”
Parry added: “One of the reasons we felt Alan did not make the impact he was expected to last year was because he missed pre-season training. He had a virus and missed most of the work.
“He did get into the side and started to look fitter. Then he sustained an ankle injury that kept him out for six weeks, so his season never really started properly.”
Mahon signed a three-year contract when he rejoined Tranmere a year ago. A product of Tranmere’s youth development system, Mahon made 144 senior appearances in his first spell before leaving Prenton Park for Sporting Lisbon in 2000. He subsequently moved on to Blackburn, Wigan and Burnley.
Parry expressed his sympathy. “Alan is the nicest lad in the world,” he said. “There is no one who feels more embarrassed when he can’t perform because he just wants to play for Tranmere and earn his corn. The sooner he gets back the better.”