Chuks Aneke's first-half goal was enough to see off Uwe Rosler's Cod Army.
Scott Golbourne returned to the MK Dons starting XI after missing the wins over Hyde United and Oxford United, while at right-back George Williams slotted into the backline in the absence of Callum Brittain.
Peter Pawlett made his first start for the club since the defeat to Blackburn Rovers in late August while Ed Upson and Alex Gilbey anchored the midfield for the men from MK1.
The first chance of the game fell the way of Fleetwood Town, Kyle Dempsey’s whipped free-kick was met by the head of Devante Cole who forced a strong save out of Nicholls. The offside flag was raised, however, Nicholls was none the wiser.
Fleetwood threatened to take an early lead after a succession of corners, however, the Dons defence stood firm with Aneke showing his defensive prowess clearing the danger a number of times.
The home sides first chance of the game came the way of Peter Pawlett, the forward heading over from Ed Upson’s corner. Pawlett once again threatened - Gilbey and Williams combined well before the Scottish international cut onto his left only for his shot to be blocked and cleared by Fleetwood Town.
With 15 minutes on the clock, Fleetwood had a golden chance to take the lead – O’Neill’s dangerous corner found Cian Bolger at the back post. Luckily for Neilson’s men – Bolger failed to connect.
Down the other end, Dons almost took the lead through a set piece of their own. Upson stood over a free-kick 30-yards from goal his delivery found an unmarked Aneke at the back post – unfortunately, the cross was just out of the forward’s reach.
The Dons had found their feet in the tie and were keeping possession of the ball while patiently waiting for gaps in the Cod Army’s defence. Williams eventually dug out a cross that looked to be perfect for Ariyibi, however, Bolger was there to clear the danger for the visitors.
The manager spoke during the week about the need for his defence to be tough to break down. Ebanks-Landell and Scott Wooton clearly heard Neilson’s comments, the pair putting their body on the line to deny both O’Neill and Burns.
After a good spell of pressure Dons took the lead on 40 minutes courtesy of Chuks Aneke - the forward displaying his relentless work-ethic in the process. After the ball bounced around the Fleetwood box, Aneke hammered home from the edge of the box past Cairns to give Dons the lead at the break.
Both sides remained unchanged at the break and there was an early shout for a penalty for the Dons. Upson’s free-kick looked to hit the hand of Hiwula. Referee Brett Huxtable ignored the calls much to the relief of Fleetwood.
Ariyibi started the second-half the way he finished the first as he continued to frustrate the Fleetwood defence. The 22-year-old cut onto his left foot before his curling left-footed strike ended up just wide of Cairns’ far post.
It took until the 58th minute for Fleetwood to threaten Nicholls for the first time in the second-half, Burns firing just over the crossbar from 25-yards out. Minutes later Ebanks-Landell once again made a last-ditch block to deny Cole from six-yards.
Agard had a great chance to extend the lead. Collecting the ball from Fleetwood's corner Ariyibi carried the ball into Fleetwood's half before playing an inch-perfect pass into the path of Agard. The striker failed to get the ball out of his feet with his strike hitting the side netting.
That proved to be the last shot on goal as the Dons stood firm defensively throughout the remainder of the second half to come away with three points.
Starting XI (4-2-3-1): Nicholls; Golbourne, Wootton, Ebanks-Landell, Williams; Gilbey, Upson; Ariyibi (Lewington 87) Aneke, Pawlett (Nesbitt 82); Agard (Seager 74).
Unused subs: Siestma (GK), Walsh, McGrandles, Thomas-Asante.
Booked: Pawlett, Ebanks-Landell.
Attendance 7,827 (128 away)