Burundi Follows Uganda’s Footsteps as Somalia’s Security Transition Faces a Dangerous Test

MOGADISHU (WDN) – Somalia is facing the prospect of another major security setback as Burundi reportedly accelerates plans to withdraw its remaining troops, following Uganda’s decision to begin pulling out forces deployed under a bilateral security arrangement. The developments come at a particularly dangerous moment: Somalia’s political institutions are deeply divided, the Federal Government is struggling to maintain control over its security forces, and Al-Shabaab is exploiting the resulting instability.

The central question is whether Somalia is capable of replacing the departing African Union forces. The answer, judging by the country’s current political and military circumstances, is deeply concerning. Rather than consolidating into a unified national force, elements of the Somali National Army (SNA) are increasingly being drawn into regional political confrontations. Some frustrated soldiers have reportedly abandoned their federal positions and joined forces aligned with their respective regions and traditional constituencies.

The consequences could be disastrous. As foreign troops prepare to leave, Somalia’s national army is becoming increasingly fragmented, while Al-Shabaab is gaining opportunities to exploit divisions within the country’s security establishment.

Burundi’s Departure Adds to Somalia’s Security Dilemma

According to Africa Intelligence , Burundi is accelerating efforts to withdraw its remaining troops before the current mandate of the African Union Support and Stabilisation Mission in Somalia (AUSSOM) expires.

Burundi has maintained a military presence in Somalia since December 2007, when its forces joined the African Union Mission in Somalia (AMISOM). They subsequently served under the African Union Transition Mission in Somalia (ATMIS) before the establishment of AUSSOM in January 2025.

For nearly two decades, Burundian soldiers have contributed to operations against Al-Shabaab and the protection of strategic locations alongside Somali and other African Union forces.

However, Burundi’s participation in the new mission became contentious following disagreements with Mogadishu over troop allocations. Burundi had proposed deploying approximately 3,000 soldiers but was reportedly allocated only 1,000 positions. The disagreement prompted Bujumbura to withdraw its commitment to the new deployment arrangement, leaving its remaining troops awaiting an orderly repatriation.

The Institute for Security Studies previously examined the financial and strategic implications of Burundi’s withdrawal, while The EastAfrican reported on the diplomatic disagreement that delayed its departure.

The withdrawal also presents logistical challenges. Burundian forces depend heavily on the United Nations Support Office in Somalia (UNSOS), which provides essential services, including fuel, food, transportation, medical assistance and logistical support. These arrangements are equally important for safely repatriating military personnel and equipment.

Uganda’s Withdrawal Signals a Wider Retreat

Burundi’s reported plans follow developments involving Uganda, another major contributor to Somalia’s security operations.

Ugandan forces have been central to the African Union’s military presence since AMISOM was established. However, Kampala has begun withdrawing troops deployed under its bilateral security agreement with Mogadishu. According to the Associated Press, the withdrawal is expected to extend to all Ugandan forces, including those serving under AUSSOM, by the end of 2027.

The departure of Ugandan troops raises serious questions about the future of security arrangements around Mogadishu and strategically important areas in Lower Shabelle.

The African Union mission has reportedly planned to take over several positions as Ugandan forces withdraw, but uncertainty remains over who will ultimately secure all the locations being vacated.

The Associated Press report highlights the funding shortages and operational difficulties complicating the transition.

The parallel developments involving Uganda and Burundi should serve as a warning to Mogadishu. Somalia cannot assume that international military commitments will continue indefinitely, particularly when the financial and political costs of maintaining foreign forces are increasing.

A National Army Increasingly Divided by Regional Politics

Perhaps more troubling than the withdrawal of foreign troops is the condition of the Somali National Army itself.

The Federal Government is supposed to be building a unified national military capable of assuming responsibility for the country’s security. Yet political disputes between Mogadishu and federal member states are increasingly drawing soldiers into conflicts that have little to do with their constitutional responsibilities.

Southwest State and Hiiraan have become particularly visible examples of this fragmentation.

In Southwest State, the political confrontation between the Federal Government and forces loyal to former regional president Abdiaziz Hassan Mohamed Laftagareen has been accompanied by reports of federal soldiers abandoning their positions and joining rival regional forces. These developments followed the federal military intervention in Baidoa in March 2026 and the subsequent struggle over control of the regional administration.

In Hiiraan, the situation has taken an equally worrying turn. Following the dispute over Hirshabelle’s leadership and the re-election of President Ali Guudlaawe, traditional leader Ugaas Yusuf Ugaas Hassan called on members of the Hawadle community serving in the national army and other security institutions to return to Beledweyne and support their community.

Subsequent reports indicated that uniformed personnel had responded to his appeal, gathering at his residence. Other reports described military personnel abandoning their existing positions and joining the mobilisation.

These developments suggest that the federal military command is facing a serious challenge in maintaining discipline and institutional loyalty. Although the precise number and status of the personnel involved remain independently unverified, the reported movements are deeply concerning.

Hiiraan Online and Critical Threats have reported on the Hiiraan mobilisation and its implications for federal military cohesion. An army whose members increasingly respond to regional and clan loyalties rather than a unified chain of command cannot reliably defend the country against an organised insurgency.

Al-Shabaab Benefits from Political and Military Disintegration

The greatest beneficiary of Somalia’s political and military fragmentation is Al-Shabaab.

While the Federal Government and regional administrations struggle over political authority, the militant organisation continues to operate, recruit, attack military positions and exploit weaknesses in security coordination.

The danger is particularly acute in areas where African Union forces have provided logistical and operational support to Somali troops. Any premature withdrawal without adequate replacement forces could expose strategic locations and supply routes to renewed militant attacks.

The United Nations Security Council, through Resolution 2809 adopted on December 23, 2025, extended AUSSOM’s authorisation until December 31, 2026. It authorised the deployment of up to 11,826 uniformed personnel, including 680 police officers, and emphasised that additional financial support was necessary for both AUSSOM and Somali security forces.

The resolution also recognised that the Federal Government bears primary responsibility for Somalia’s security.

The UN Security Council resolution makes clear that the transition requires sustained international support and stronger Somali security institutions, not simply the departure of foreign forces.

Yet the political and military developments inside Somalia raise doubts about whether the country is prepared to meet that responsibility.

Mogadishu Cannot Replace Foreign Forces Without First Fixing Its Own Army

The Federal Government faces a fundamental contradiction. It wants Somali forces to assume full responsibility for national security while simultaneously deploying those forces in domestic political confrontations that undermine their unity and credibility.

The national army cannot become a reliable successor to AUSSOM while soldiers are being drawn into disputes between Mogadishu and regional administrations. Nor can the government expect international partners to maintain confidence in its security transition when the military is increasingly vulnerable to competing political and communal loyalties.

Somalia urgently needs a national security consensus that separates the armed forces from political rivalries, restores a professional chain of command, ensures regular salaries and logistical support, and establishes clear agreements with federal member states over military responsibilities.

Without these reforms, the withdrawal of foreign troops risks creating precisely the security vacuum that Al-Shabaab has spent years trying to exploit.

The danger is not simply that Burundi and Uganda may withdraw their forces. It is that they could leave behind a security vacuum that Somalia’s divided political leadership and increasingly fragmented national army are incapable of filling.

After nearly two decades of international military assistance, Somalia should be moving towards greater security independence. Instead, the country risks entering another dangerous phase in which foreign forces are departing, national military cohesion is deteriorating, and Al-Shabaab is gaining strategic opportunities.

The greatest threat to Somalia’s security transition may therefore be less about the number of foreign troops leaving than the absence of a functioning national political and military framework capable of replacing them.

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