The Pilgrims scored three superb goals through Kari Arnason, Chris Clark and Onismor Bhasera - who also netted an own goal - to end the Dons' three-match winning run at stadium:mk and climb to 13th in League One.
Bhasera finished a swift breakaway to put Plymouth ahead after 22 minutes, running at Gary MacKenzie before lashing a rising shot into the top corner from the edge of the box.
- League One: As it happened
- League Two: As it happened
Dons goalkeeper David Martin pushed Joe Mason's strike around the post but was then fortunate to see Arnason slice wide from close range after flapping at Bhasera's corner.
But Arnason made amends by blasting a dipping shot in off the underside of the crossbar from 35 yards to double Plymouth's lead in the 29th minute.
The lacklustre Dons were thrown a lifeline six minutes before the break when the sliding Bhasera inadvertently diverted Danny Woodards' low cross into his own net.
Bhasera then cleared Mathias Doumbe's header off the goal-line on the stroke of half-time.
Martin produced a superb double save to deny Yannick Bolasie and Mason after the break before Clark sealed the win 10 minutes from the end, sweeping home substitute Jim Paterson's low cut-back from the edge of the box.