Ten-man Pompey Academy lose after conceding second-half penalties
The young Blues went 2-0 down in the first half but managed to level the scoreline before half-time.
But two spot-kicks for the visitors and a red card for Josh Flint saw Pompey drop to defeat.
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Hide AdMK Dons took the lead within the first 10 minutes after applying early pressure.
They then furthered their lead on 20 minutes.
But Pompey pushed up the field and were awarded a penalty late in the first half.
It was converted by striker Matt Mayes.
Then, just before the break, Leon Maloney equalised for the hosts.
But early in the second half MK Dons took the lead again.
The visitors were awarded a penalty and Flint was sent off for Pompey.
The match was put beyond the Blues when they conceded another spot-kick late on and the game finished 4-2.