Flights were launched in December and were due to run until 23 April but will cease on 16 February.
The airline said: “This winter, changing travel restrictions and arrival testing requirements set by the UK and Scottish governments led to subdued bookings on the route. Following careful review, we’ve taken the difficult decision to shorten the existing Edinburgh-Barbados schedule.”
The service, which was scheduled to be winter-only, will return as planned on 12 December, with seats already on sale.
A Virgin spokesperson said: “Affected customers will be contacted in the coming days with their options, including the choice to convert their booking to a voucher or request a full refund.
“If rerouting is a suitable option, we can also rebook customers on alternative Barbados services from Manchester or Heathrow. Those who booked via a third party such as a travel agent should contact them directly for their options.”
Virgin said it would proceed with the launch of twice-weekly Edinburgh-Orlando flights from 30 March 2022.