Both players were forced off with injuries during the 1-1 draw at Carlisle on Saturday.
Dons boss Karl Robinson said: "It's the story of our season. David Martin was a big miss to us, and to lose Gary MacKenzie at the end was a big loss to us too.
"But we have to keep looking forward and keep positive. I have to patch the team together, but I can only work with the players I have available. We're still a long way from putting our best team on the pitch.
"We didn't have a fit winger on Saturday - Daniel Powell wasn't really fit enough but we threw him on to make a difference in the last 20 minutes. It's difficult when you can't make subs that can make a difference."
Should Martin miss out, 21-year-old Ian McLoughlin will make his first league start of the season for the Dons.
Former Pompey striker Izale McLeod will battle it out with Ryan Lowe for a place in attack while fellow striker Alan Smith serves the second game of his four-match suspension.
Winger Dean Bowditch (groin) and long-term absentee Stephen Gleeson (broken foot) remain unavailable.