The operation deployed to Somalia soon after the Islamic Courts Union was deposed by troops from Ethiopia during a large scale invasion in late 2006.

The duration of AMISOM's mandate had been extended in each period that it has been up for review, until it was replaced on April 1, 2022, by the African Union Transition Mission in Somalia.

[14] As early as 25 March 2005 the Islamic Courts Union (ICU), a rising Islamist group fighting warlords in Mogadishu, warned that any foreigner peacekeepers deployed to Somalia would be unwelcome and face death.

The African Union's involvement in the war came at the insistence of both Ethiopia and the United States for the organization to take over the role of ‘regime changer’.

During 2007, the operation relied heavily on Ugandan Peoples Defence Forces (UPDF), as Uganda played a crucial role in offering support to the initiation of the mission.

[23] The European Union was reportedly 'exceptionally unhappy' about the heavy US support for the December invasion, and held back funds for the newly created AMISOM mission for several months.

Because of the objection of the burden falling on these three nations alone (and the rivalry between Ethiopia and Eritrea), the mission was expanded to include other member states of the African Union.

[34] Following the defeat of the Islamic Courts Union in December 2006 – January 2007 the international community began to gather both fiscal commitments as well as military forces for the mission.

[5] On 22 January 2007 Malawi agreed to send a half-battalion to a battalion (ranging widely anywhere between approximately 400 to 1,200 troops) for a peacekeeping mission to Somalia.

[40] On 2 February 2007, the United Nations Security Council welcomed the advent of the African Union and Intergovernmental Authority on Development-led peacekeeping mission.

[42] On 9 February 2007 a gathering of 800 Somali demonstrators in north Mogadishu, where Islamist support was strongest, burned U.S., Ethiopian, and Ugandan flags in protest of the proposed peacekeeping mission.

[51] On July 28, 2009, the World Health Organization was notified that 21 AMISOM soldiers in Mogadishu had become sick, and three had died, with acute peripheral edema, difficulty in breathing, palpitations, and fever.

[53] A few days later in response to UN pressure, the AU agreed not to expand the mandate but did allow preemptive strikes against Al-Shabaab and promised more troops from other African countries.

[58] AFP, reported in Africa Research Bulletin, said Burundian military chief General Godefroid Niyombare said on 14 March 2011 the soldiers had been deployed a week before.

[60] During the same month, AU Commander Fred Mugisha suggested that Al-Shabaab was "at [its] weakest" and would likely "implode in the not so distant future" owing to successive military defeats that it suffered as well as an exodus toward the Arabian Peninsula of hundreds of the group's fighters.

[61] Due to the successful military operations against the Islamists, the United States has also been stepping up efforts to train and equip the AMISOM troops in a bid to stamp out the Al-Shabaab insurgency and limit its influence.

Personnel (J1) would be led by the AU, with Kenya taking responsibility for intelligence (J2) and logistics (J4), Uganda operations (J3) and engineer (J8), Burundi plans (J5) and communications/IS (J6), Sierra Leone training (J7), and Djibouti CIMIC (J9).

[66] On 9 August 2013, an Antonov An-24 operated by the Ethiopian Air Force crashed while attempting to land at Aden Abdulle International Airport in Mogadishu.

[67][68] The flight departed from Dire Dawa International Airport in Ethiopia at 06:00 local time that morning, commanded by Colonel Berhanu Geremew, a highly experienced pilot.

[72] Analysts suggested that the move was primarily motivated by financial considerations, with the Ethiopian forces' operational costs now slated to be under AMISOM's allowance budget.

[75] From June 2021 to March 2022, the EU and its allies reimbursed Kenya nearly Sh2.54 billion, in quarterly disbursements Sh811 million, for its continued military participation in AMISOM.

On 7 October 2015, Francisco Caetano Jose Madeira, of Mozambique, was appointed to this position, replacing Maman Sambo Sidikou of Niger.

[197][198][199] By January 2017 the Burundi government threatened to withdraw its forces from Somalia altogether, arguing that these were a national contingent and not mere mercenaries, as would be suggested by the troops receiving payment directly from any third party.

In April and May, members of Task Force Raptor, 3rd Squadron, 124th Cavalry Regiment of the Texas Army National Guard, took part in a separate training mission with the BNDF in Mudubugu, Burundi.

In June 2012, U.S. Army Africa commander Major General David R. Hogg spoke encouragingly of the future of Sierra Leone's forces in conjunction with Kenya.

"Bancroft Global Development, headquartered on Washington's Embassy Row, employs about 40 South African and European trainers who work with [AMISOM's] Ugandan and Burundian troops.

[240] Bancroft director Michael Stock told The EastAfrican that these mentors are embedded with AMISOM units in Mogadishu and southern and central Somalia.

Western-backed African Union troops in Somalia gang-raped women and girls as young as 12 and traded food aid for sex, Human Rights Watch has said.

An investigation uncovered evidence of sexual exploitation of women seeking medicine for sick babies at what they assumed was the safety of AU military bases.

Human Rights Watch documented cases in a 71-page report published on 8 September 2014 with recommendations to the African Union, the United Nations, the Somali government and AMISOM donors UN, EU, UK and US.