Allen took over from Graham Westley in March. The Bees won 16 points from eight games under the 52-year-old.
“A short while ago I had a meeting with the chairman Tony Kleanthous to let him know that I would not be continuing to manage his club and your club,” Allen told the club website.
It’s been an amazing, unforgettable 8 weeks with all the players and the positive energy and the enthusiasm from all the supporters has been quite overwhelming and I can’t thank you enough.
The Chairman has offered me a fantastic contract, offered to increase the budget and had done everything he could and no blame what so ever can be put his way. For me, it was 8 weeks and I am happy but of course underneath I’m bitterly disappointed and still very upset that we were unable to retain our position in the Football League.
I really do hope Barnet Football Club can now grow with these players plus the addition of Johnson, Tarpey and Vilhete and you can all be proud to be Barnet supporters.