Alex Cruz, chairman and chief executive British Airways, is to step down from the roles with immediate effect.
He will remain with the airline as non-executive chairman.
The decision comes weeks after British Airways-owner International Airlines Group saw chief executive Willie Walsh step down to be replaced by Luis Gallego.
Commenting on the news, Gallego said: “I want to thank Alex for all that he has done at British Airways.
“He worked tirelessly to modernise the airline in the years leading up to the celebration of its 100th anniversary.
“Since then, he has led the airline through a particularly demanding period and has secured restructuring agreements with the vast majority of employees.”
He added: “IAG has proved itself to be one of the leading airline groups in the world with a portfolio of successful companies.
“We are navigating the worst crisis faced in our industry and I am confident these internal promotions will ensure IAG is well placed to emerge in a strong position.”
Cruz will be replaced by Sean Doyle, currently Aer Lingus chairman and chief executive.
He will become the new chief executive of British Airways immediately, and take over as chairman after a transition period.
Fernando Candela, currently chief executive of low-cost IAG subsidiary Level, is also joining the group management committee in the new role of chief transformation officer.
Gallego added: “Sean Doyle has extensive experience at British Airways having worked there for 20 years before moving to head Aer Lingus nearly two years ago where he has done an excellent job.
“I am confident that will continue at British Airways.
“Fernando Candela, who has more than 25 years of experience in aviation and excelled at both Iberia Express and Level, joins our management committee in the new chief transformation officer role.
“He will coordinate change across the group, focusing on creating a company fit for a different future and ready to take advantage of new opportunities.”
Candela will also remain chief executive of Level until a replacement is appointed.
At Aer Lingus, Donal Moriarty, currently chief corporate affairs officer, will become interim chief executive.
A permanent appointment will be announced in due course, IAG added in a statement.