Flybe is replacing its Rewards4All frequent flyer scheme with the International Airlines Group-backed Avios scheme.
The new arrangement comes into force from October 27 as the airline seeks to offer improved benefits to passengers.
Rewards4All members are being told they will need to redeem their outstanding points within six months from today’s announcement.
Redemptions can be made on flights up until October 24.
The Avios partnership begins on the day the regional carrier starts flying from London City airport with daily flights to Edinburgh, Belfast, Aberdeen, Dublin, Inverness and Exeter.
The deal follows recently announced partnerships with Booking.com and STA Travel, which has established Flybe as preferred partner for student and youth travel.
Flybe chief executive
Saad Hammad said: “This agreement represents a significant service enhancement for Flybe customers – a big step change that opens up a new world of reward possibilities.
“We join Avios following an extensive review of frequent flyer programmes, including our own in-house programme Rewards4All.
“We determined a better customer proposition existed, and the clear choice was Avios. There are two million customers with billions of Avios within 30 miles of a Flybe airport. ”
Avios managing director Gavin Halliday said: “This is an important partnership for Avios, building on our commitment to provide engaging collection and redemption opportunities for Avios Travel Rewards Programme members.
“Our members will benefit from access to even more reward flights and on new regional routes, as well as the new opportunity to collect when flying with Flybe.”
Avios operates the global Avios currency for the British Airways Executive Club, Iberia Plus and Meridiana Club frequent flyer programmes as well as the Avios Travel Rewards programmes in the UK and South Africa.