The winger spent the first half of the season at Fratton Park from QPR.
However, Wheeler struggled for regular first-team minutes at the Blues and was behind Jamal Lowe, Ronan Curtis and Andre Green in the pecking order.
The 28-year-old made 19 appearances for Kenny Jackett's side and scored two goals – one being the winner in the 1-0 Checkatrade Trophy quarter-final win over Peterborough.
But the former Exeter man was handed just a solitary start in League One before returning to Loftus Road in January.
Wheeler subsequently moved to the Dons and played a key role in their promotion.
He netted four times in 18 matches, grabbing the crucial goal against Mansfield on the final day of the campaign.which saw Paul Tisdale’s side leapfrog the Stags into third.
Wheeler wrote on Twitter he was ‘over the moon’ – a post that was liked by former Pompey team-mates Christian Burgess, Jamal Lowe and Danny Rose.
He said: ‘Over the moon to achieve promotion with a great group of lads @MKDonsFC.
‘It's been a tough year or so, but proud to have played my part. Bring on the summer!!!’