The 20-year-old's previous contract was due to expire at the end of the season, but the club have moved to tie him down to a deal to keep him at the club until 2015.
Dons boss Craig Brown was delighted to keep hold of the Irishman as he is highly-rated at the SPL outfit.
"Joe has signed a new deal for two years which is great for the club," said Brown.
"He has done very well in the games he has started in recent weeks. I expect him to really push on."
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