NATO began providing support to the African Union Mission in May 2005 and the approach in Africa is based on recognition of the African Union's desire to provide African solutions to African problems. As such, all assistance is based on specific requests from the African Union. Initially, it was focused on providing logistical support for the African Union Mission in Sudan, or AMIS. When AMIS transitioned to the hybrid United Nations and African Union Mission in Darfur, or UNAMID, NATO nations had provided airlift for 32,300 personnel.

SHAPE delegated the authority to Joint Command Lisbon to have the operational lead for NATO engagements with the African Union. They provide the majority of the personnel to support the mission, to include the Senior Military Liaison Officer 1 OF-5 (Colonel), or SMLO. The SMLO is co-located with the AU HQ in Addis Ababa, Ethiopia and he provides NATO's daily interface with the AU and is also responsible for representing NATO to other partner nations and organizations, like the EU, which also maintains an office in Addis Ababa.

NATO now has a standing agreement to provide Strategic sealift and airlift support for African Union Troop Contributing Countries willing to deploy to Somalia. The first request was received in June 2008 to transport a battalion of Burundian peacekeepers to Mogadishu and, the second and last one was in Feb 10 when AU requested strategic airlift support to rotate Ugandan and Burundian units of the African Union Mission in Somalia (AMISOM). The NATO sponsored, USA contracted, DynCorps International airlift sorties commenced on 5 Mar 10 from Entebbe to Mogadishu and transported approximately 500 of the 1,700 personnel into Somalia as well as approximately 300 troops back to Uganda.