A Nicky Rizzo thunderbolt and Wade Small's brace sent Milton Keynes above the Welshmen in the table, who were docked 10 points in midweek for going into administration.
The Dons came out bursting with confidence and a new found enthusiasm after Wilson's appointment in midweek, and it was no surprise when Rizzo finished a fantastic flowing move with a sweet strike into the top corner in the seventh minute.
The in-form Wade Small broke down the right, and after a neat interchange involving Allan Smart, Gary Smith slotted a killer ball through to the former Crystal Palace man who made no mistake from 15 yards.
Dons continued to string together some nice passing moves after the opening goal and Smith and full-back Dean Lewington were unfortunate not to double the lead as Wrexham were reeling.
But the Red Dragons found their feet midway through the first half and Dons keeper David Martin was lucky to get away with dropping a cross a at the feet of Juan Ugarte, whose effort was blocked by a wall of determined Milton Keynes defenders.
However, after coming close to an equaliser, Wrexham were glad to still have 11 men on the pitch minutes later as captain Dennis Lawrence hauled down Izale McLeod as he raced through on goal.
A clever ball by Smart put the Dons' top scorer away, but Lawrence escaped with only a yellow card as McLeod looked set to double the home side's advantage.
Small's fierce 20-yard drive forced a sprawling save from Wrexham keeper Andy Dibble as the first half drew to an eventful close.
The Dons picked up where they left off after the interval and Small made it 2-0 just five minutes into the second half.
The pacey forward turned Lawrence inside out on the edge of the box and, after Dibble blocked his first effort, a fortunate break sent the ball trickling towards the goal-line for Small to tap home.
Wrexham should have pulled one back four minutes later when former Norwich man Chris Llewellyn blasted against the bar from just eight yards as the Dons defence went to sleep.
Red Dragons' boss Dennis Smith threw on former £4.5million Tottenham striker Chris Armstrong, Alex Smith and pushed Llewellyn up front in a bid to get his side back in the game.
But after withstanding a heavy aerial bombardment, Milton Keynes hit Wrexham with a killer third goal five minutes from time.
Substitute Alex Tapp's clever ball put Small clean through, who slotted his fifth goal in seven games past the exposed Dibble to complete the rout.