The former Leeds, Manchester United and Newcastle striker has been handed the role of player-manager for the quarter-final tie.
Dons assistant boss Mick Harford was initially set to be in charge during the competition but there has been a change after the game, which was initially scheduled for December 12, was postponed due to a frozen pitch.
Arsenal legend Ian Wright, the club's first-team coach, will assist Smith from the sidelines.
Dons manager Karl Robinson told the club's official website: "As the manager of this club it is my job to develop the players but also the coaching staff too.
"Alan is keen to get his hands dirty and while he is still a key player for us, I think this is an excellent opportunity for him to see the other side of the game with Wrighty.
"It is their chance to take control of the match and use their tactics while myself and Mick watch on with interest from the stands."
The game at Aylesbury will kick-off at 7.45pm with the winners set to face Beaconsfield in the last four.