Current CCO Jochen Schnadt, who has been with the company for three years, will become managing director on October 11.
He takes over from Tim Shattock who joined flybmi as interim managing director earlier this year to assist in its managerial transition process.
Shattock will now return to his native Dublin to take up a new leadership role.
Flybmi said the restructure would help to “better address the key needs” of its business going forward.
A “key part” of this organisational adjustment, flybmi said, would be the appointment of Malcolm Sutherland, the airline’s new chief operations officer.
He will oversee all operational functions of flybmi, reporting to Schnadt.
In addition, Schnadt will continue to have the directors for sales and business development, Fabrice Binet, revenue and planning, Barry Oaten and customer and marketing, Antony Price, reporting to him alongside chief financial officer, Paul Roberts and head of people, Suzanna Smith.
Meanwhile Peter Bond, co-owner of the airline, will assume the position of co-chairman of parent Airline Investments Limited, taking on “a more active role to further strengthen the day-to-day running” of flybmi and sister airline Loganair.
Flybmi operates a 19-strong all-jet fleet with primary hubs at Bristol, Munich and Brussels.
Schnadt said: “I feel very privileged to have been asked to take on the managing director role and to be able to work with the great team that we have to move things forward to the next level.
“I am also delighted to welcome Malcolm to the team, who, with his previous experience in Virgin Atlantic and the Thomas Cook Group, will add tremendous value to the Team and effort at flybmi, joining us at this very exciting time.”