A niggling injury hampered Bowditch towards the end of last season but it is hoped the 27-year-old's surgery will clear up the problem.
Simon Crampton, head of sports medicine at the Dons, told the club's official website: "Unfortunately, Dean had a recurrence of a groin injury.
"Following a detailed assessment period and consultation with a specialist surgeon in London it was decided that the best option would be to perform a small surgical procedure to rectify the problem.
"He is expected to make a full recovery and we anticipate he will return to training in August."
Bowditch will fly out to Dublin later this week to start an intensive rehabilitation programme with the Dons' medical team.