The Essex-based carrier confirmed that it was scrapping three connections from Glasgow Airport - to Cardiff, Paris Charles de Gaulle and Shannon - from January next year.
It also confirmed that a summer-only service from Edinburgh to Knock, in Ireland, would be withdrawn.
Passengers affected by the changes are being contacted and will be offered an alternative flight or a full refund, the company said.
The announcement came as the airline outlined its summer 2014 schedule.
The cuts come weeks after Flybe announced it would be closing bases at Aberdeen and Inverness as part of an £85 million cost-saving drive, which will also see around 500 staff axed across the UK.