The in-form Dons travelled to Shropshire having won their last three games.
But an incredible opening 20 minutes saw Town race out the blocks and into a 3-0 lead.
A Sean Goss goal and penalties from Ollie Norburn and Curtis Main put them in a commanding position at Montgomery Waters Meadow.
The visitors pulled a goal back through Will Grigg before Goss netted a second shortly after the re-start to restore Salop’s three-goal cushion.
And while substitute Charlie Brown netted another consolation for the Dons, there could be no doubt Shrewsbury deserved all three points.
Once again Wilbraham was the man on the touchline with boss Steve Cotterill at home recovering from Covid-19.
And the assistant boss had nothing but praise for Town’s players.
“It was a great team performance,” he said.
“Our plan worked. The gaffer gives us the detail for the game plan and we all worked hard to do it.
“The boys work rate, discipline and decision making - everything we talked about was perfect.
“We could have got more goals and that is because it was a great team performance with everybody working hard for one another.”
Wilbraham was pleased with the way Shrewsbury’s players managed the game having gone 3-0 up.
But while Cotterill too was delighted with the overall performance, he revealed the boss told the players - via video - he wasn’t happy with the goals they conceded.
Asked about scoring three goals inside 20 minutes, Wilbraham said: “It can sometimes be difficult then because it’s an unusual position to find yourself in.
“I think we managed it really well.
“We were still unhappy with the goals we conceded and the manager touched on that post-match.
“We know MK are going to try and dominate possession and they make you do a lot of running.
“But we knew we would create chances if we stuck to the game plan, were disciplined and backed each other up on the counter-attack.”
Norburn scored Salop’s first penalty after eight minutes but it was Main - who grabbed his first Town goal - who scored the second.
And Wilbraham had no problem with the change of penalty taker.
“I don’t think that’s a bad idea when there are two close together like that,” he added.
“Norbs stuck the first away but Curtis had asked for it.
“He is a centre-forward who wants a goal. He had a couple of assists and worked really well for the team but he wanted that goal.
“Norbs wanted the first one but when we got the second he ran over the bench and said Curtis wanted it, is that okay?
“And we said, ‘yeah - it’s up to you boys.’
“We are happy for them to sort it out. You see some teams arguing about it but it was just a great choice from Norbs, the captain, telling Curtis to go and get himself one.”