Richie Barker left the team-talks for new manager Robbie Neilson during the 0-0 draw with Charlton.
After Neilson was unveiled as Dons boss on Friday, Barker remained in charge for the trip to The Valley.
But the new boss, who watched over the game from the director's box, led the team in the dressing room as Barker admitted he took a back-seat.
He said: "He left most of the pre-match to me, I did the training. But he did the talking before the game and he took half time. I didn't even go in the dressing room. I believe if there are too many voices, it can confuse things.
"It's his club, now. And at the end, I just thanked the players for their efforts."
After eight games in charge, he couldn't quite sign off with a victory - ironically against his old manager Karl Robinson in the Charlton dugout. Dons had the best chances too, with George Baldock, Kieran Agard and Dean Bowditch all having excellent opportunities to book Dons' spot in the third round.
Barker said: "I thought we deserved to win the game. We were by far the better team in the first half and arguably had the best chance in the final minute. I don't think there's any doubt that we were the best team and should have won it.
"Charlton had chances too today, but goal-scoring has been our issue all season and was the issue today too. It is the problem of the season."
Barker's name rang out from the travelling MK Dons supporters throughout the match, as did that of Neilson and indeed Robinson.
"It was a great moment," said Barker. "I want to thank the fans for their support over the last six weeks.
"Hopefully they'll see the benefits of what I've had to do. It was very humbling - when you're an assistant, you keep out of the limelight. It was nice that I got an opportunity to sign off in that way too."
But with Neilson bringing assistant Stevie Crawford from Hearts to join him in the Dons backroom staff, Barker admitted he isn't sure where his future now lies.
"I honestly don't know. I'll come in on Monday, talk to who I need to talk to and take it from there.
"I've done my bit, I won't be getting in the way. It would be tough for them to have me on the training ground."