The Chadian is poised to take over from South Africa’s Nkosazana Dlamini Zuma.
Mahamat was welcomed by both AU and Ethiopian officials as he arrived at Bole international airport.
A series of events are scheduled to follow the handover process.
The Chadian foreign affairs minister beat Kenya’s Amina Mohammed and Senegal’s Abdoulaye Bathily in the January vote to win the AUC’s chairperson seat.
He is however, not new in the workings of the AU. He has previously served as the body’s chair of the Economic, Social and cultural council.
Mahamat has been at the forefront in the fight against Islamist militants in Nigeria, Mali and the Sahel.