The Scholars slipped to a fifth consecutive defeat despite having much of the play in an entertaining game.
Brad Sach almost opened the scoring for the home side on 17 minutes but a great save from visiting 'keeper Henry Newcombe kept the scores level until late in the first half.
With five minutes to the half time break George Nicholas was unlucky not to give Potters Bar the lead but his long range effort came back off the "woodwork" with the 'keeper well beaten.
Just two minutes later Margate were in front with George Brown taking advantage of a defensive slip to nip in and slot home to give the visitors the half time lead.
With almost an hour gone Margate doubled their lead as the home defence failed to to deal with a right wing cross with defender Jack Paxman heading home the rebound.
Potters Bar got back in the game with Sean Grace rising to head home a Keagan Cole free kick.
The Scholars continued to push for an equaliser but it was Jordan Robins for Margate who went closest to adding to the scoreline with his long range effort hitting the bar.
Updated 01:06 - 3 Dec 2018 by Jeff Barnes