Mahon last played against Leeds on February 19, scoring his seventh goal of the season and turning in an impressive display in the centre of midfield.
Although he reported no discomfort in his knee during the game, it swelled up painfully the following day, and the specialist found he had a cyst at the back of the joint which was filling with fluid and a rest period has seen the problem clear up.
Manager Paul Jewell said: "Alan is back training with us and looks like he is getting over the injury.
"He was playing well before he was hurt and it's important we have as many players available to us over the next few weeks.
"There is a part to play for everyone and all the lads need to be ready if they are called upon before the end of the season."
The best Mahon can probably hope for next week, though, is a seat on the bench following the signing of Graham Kavanagh during his absence.
Kavanagh has settled well following his £350,000 switch from Cardiff, forming a promising partnership with Jimmy Bullard.
Jewell said: "Kav has been a good signing for us, a calming influence, and when I was talking to Lennie Lawrence (Cardiff manager) the other day, he thought we now had the best midfield in the division.
"I don't think too many people could argue with him."
The injury news wasn't quite as good for centre-half Emerson Thome who hasn't appeared since the game at Crewe.
He strained his hamstring muscle that February 12 afternoon and has since injured a calf muscle during his rehabilitation work.
Jewell said: "Emo still has a lot of work to do because he has been missing for over a month now, so I can't see him being ready for West Ham."
Mahon and Thome have been the two main injuries recently, although Jewell reported a number of players were suffering minor bumps and bruises.
For that reason, he is pleased to have the fortnight break between matches.
Jewell said: "John Filan has been carrying a knock, the Duke has a couple of injuries as has Jason Roberts.
"I think the break has come at the right time, particularly as we normally play two matches in a short space of time over Easter.
"The lads have had a bit of a breather this week, we've thrown in a couple of training sessions too, but come Monday, it's full on again for the West Ham game."
Latics' Championship clash with leaders Sunderland at the JJB Stadium on Tuesday, April 5, is now all-ticket.
Sunderland have already sold 5,000 of their 7,400 ticket allocation.
The West Ham United home game on April 2 is also an all-ticket affair.
Tickets are now on general sale for both games.
Third-choice goalkeeper James Salisbury is back from a loan spell at Halifax Town after he dislocated his shoulder at the weekend.