The BBC understands that Flybe had been talking to Newquay airport about measures that might mitigate the effects of the change to Gatwick.
Senior industry sources confirmed said the decision to move had now been made and the airline's website has for some time not been selling Newquay-Heathrow flights past the end of March.
The route will, however, still qualify for public subsidy.
Separately, the BBC has learned that Flybe will, also from the end of March, be free to divert many of the Heathrow runways slots it uses for domestic flights to other short-haul services. Flybe was awarded the slots in 2017 as part of "remedy" imposed by competition regulators on British Airways after it bought BMI British Midland.
BA had to surrender the slots - which are highly prized, with pairs selling for £20m or more - as long as the new owner operated them on certain domestic routes. Flybe is, however, free to change to other short-haul routes from the end of March.
Industry sources said it could use those slots for European flights currently operated by its partner airlines - leaving one of its shareholders, Virgin Atlantic, or its partner Delta Air Lines of America, the chance to start new long-haul services from Heathrow.
BBC - Flybe to switch Newquay-Heathrow flights to Gatwick