Liam Millar's first-half goal condemned MK Dons to just their third defeat at Stadium MK this season.
The Liverpool loanee's strike 27-minutes into the tie was enough to see the visitors return to London with a win under the belft. Martin's side dominated possession and had majority of the chances after the break, but Charlton were organised in their approach as they held out for all three points.
The defeat leaves MK Dons 16th in the Sky Bet League One table ahead of Saturday's clash with AFC Wimbledon.
Russell Martin made two changes from the team that ran out 3-1 winners over Fleetwood Town last Tuesday. Both Harry Darling and Matt O'Riley were handed their first starts in an MK Dons shirt, replacing Regan Poole and Lasse Sorensen respectively. The Dons were also boosted with the return of Louis Thompson who was involved in the Matchday squad for the first time since November.
The first chance of the game fell the way of Charlton's Jayden Stockley. Having picked up the ball inside MK Dons' half, he tried his luck from outside the box, Fisher reacted well to deny the visitors an early lead.
Although the opening stages of the game didn't have many chances, it was the visitors who took the lead. Conor Washington's cross into the box was missed by Stockley, however, Liam Millar was lurking unmarked at the back-post. The Canadian set himself before hammering home to give his side the lead. 0-1.
The Dons looked for an immediate reply with both Scott Fraser and Matt O'Riley central to their attack. The duo combined well from a corner as O'Riley fired narrowly over from inside the box.
O'Riley then picked out the run of Mason from the Dons next corner. His header clattered the post before Charlton were able to clear their lines.
Laird then beat his man to pick out the run of Joe Mason. Although the cross was behind the striker, he shifted his body well to chest into the path of O'Riley. His powerful effort was blocked by Jason Pearce.
As the first-half drew to a close, Ben Gladwin had his first effort of the night. The midfielder eased pass two Charlton midfielders before firing wide from outside the box.
Shortly after the break, Ethan Laird was clattered on the edge of the box by Conor Washington. Although the Charlton man wasn't booked, the referee did award a free-kick in a dangerous position. Both Gladwin and Fraser stood over the ball, with the latter hitting the wall.
Fisher made his first save of the second-half as he got down well to deny Millar as he broke through on goal down Charlton's left.
Lewington then created a chance for MK Dons, the Dons captain done well to beat two men before threading into the path of Laird. It looked as if the right-back would level the scoring, but Amos was quick to react and smother at his feet.
The Dons were certainly dominating the second-half, Gladwin was the latest man to go close, he dragged wide from a free-kick. He then produced a delicate cross for O'Hora, who saw his header rebound off the crossbar.
More chances fell the way of Russell Martin's side, this time Laird forcing Amos into a save from Amos' corner.
Having replaced Ethan Laird with 10-minutes remaining, Matthew Sorinola saw a deflected effort land narrowly over the bar.
The final chance of the game fell the way of MK Dons as Charlie Brown broke the offside trap. Having got in behind he looked to pick out Fraser, but Charlton were on hand to clear.
MK Dons: Fisher, Lewington, Darling, Gladwin (Brown 80), Fraser, Laird (Sorinola 80), O'Hora, O'Riley (Thompson 64), Mason, Harvie (Poole 80), Jerome.
Subs: Nicholls, Sorensen, Johnson.
Booked: O'Riley, Thompson.