It was an even affair with both sides level at the break, but moments after the restart the Dons took the lead and added a further two towards the end of the game.
Youth Team coach Danny Webb made two changes to the starting XI that won in the FA Youth Cup last week as Eric Lopes and Hector Kyprianou stepped into the side with Sam Dalby and Ruel Sotiriou away with the first team.
A bright start from Orient saw them hit the woodwork with their first attack. Eric Lopes found space and curled an effort towards goal only to see it bounce back off the crossbar.
Shortly after the opening chance the O’s went close again, this time Toby Stevenson’s flick from Charles Clayden’s corner flashed across the face of goal, only needing a touch to be converted towards goal.
The visitors first chance came after a cut in from the wing provided their midfielder with space to shoot, but again his attempt came back off the crossbar before being cleared away from danger by O’s defenders.
After a quiet 10-minute spell where possession was shared equally, the visitors came close to taking the lead. The Dons striker raced through on goal with only ‘keeper Arthur Janata to beat, but Andrew Camilo-Tayaca’s brilliant recovery allowed him to make a tackle before Janata collected gratefully.
After the restart, Janata made an excellent save to deny the winger a goal, after he cut in and fired towards goal.
However, the O’s couldn’t clear the danger and Bradley Bell converted a cross from close range to open the scoring for MK Dons.
Almost immediately the visitors were in on goal again, but a recovering tackle from Stevenson was enough to put the striker off before Janata closed him down and gathered the ball well.
Being a goal down Orient stepped up their search for an equaliser and applied pressure on their opponents. The O’s thought they were level through an own goal when the Dons defender headed into his own net from a free-kick, but the referee ruled the goal out for a foul in the box.
Ten minutes remained when the visitors grabbed their second through Recoe Martin, who tapped home from the six-yard box after Janata’s initial save fell into the midfielder’s path.
MK Dons stretched their lead moments before the whistle, a deflected clearance gave Dylan Asonganyi a clear run at goal before he slotted into the bottom corner to give the hosts their third of the day.
ORIENT: Arthur Janata, Andrew Camilo-Tayaca, Teddy Perkins, Toby Stevenson, Alfie Fleming, Ernold Haxhiu, Hector Kyprianou, Eric Lopes, Amin Benyoucef, Charles Clayden, Jaedon Phillips
SUBS: Samuel Amedu, Luca Carter-Henry, Brendon Shabani, Will Sanders