Flybe was the company's only remaining customer, leaving it with no other choice but to cease operations, a spokesman said.
It is believed Aurigny staff will take on the handling for Flybe –whose services are now operated by Blue Islands under a franchise agreement, except for Birmingham and Exeter.
'This decision has led us to announce the closure of our operations there with effect from 26 September 2016,' said a Menzies Aviation spokesman.