Violence quickly enveloped the city in late December 1990, during the Somali Civil War, and on 1 January 1991, the ambassador contacted the State Department to request the closure and evacuation of the embassy.

Approval was given the following day, but violence and the collapse of the central government prevented the US, and several other countries, from airlifting their diplomats and civilians through Mogadishu International Airport.

In December 1992, the embassy compound was reoccupied and repaired to serve as a headquarters for US personnel within the Unified Task Force and, following the transition to UN control, a base for UNOSOM.

[12] In addition to establishing a presence, the consulate staff were also charged with political research and developing relations with future Somali leaders.

[13] The consulate-general was elevated to embassy status[10] and its Chargé d'affaires, Andrew G. Lynch, was appointed ambassador on July 5.

[13][14] Like most US diplomatic posts in Africa during the Cold War, a primary purpose of the embassy was to counter Soviet influence in the region and contain the spread of communism.

[16]: 15–18 During the 1969 coup d'état which brought Siad Barre to power, the embassy was blockaded by soldiers, who prevented the movement of persons into or out of the compound for over 24 hours.

[11]: 39 In the late 1980s, there was increasing rebellion against the rule of President Siad Barre and by 1990, the country began to descend into civil war.

[23] Ambassador Bishop also gained valuable experience organizing evacuations of several embassies in the 1980s while serving as Deputy Assistant Secretary of State for Africa.

[17]: 75–78 Aware of the violence going on in the Somali countryside, Ambassador Bishop felt "the odds were better than even that we would have to leave Mogadishu under less than favorable circumstances.

"[17]: 85  On August 1, Ambassador Bishop visited United States Central Command—the military command for the Middle East and Northeast Africa[b]—where he worked with military experts to review the embassy's Emergencies and Evacuation (E&E) plan until he was "satisfied...that [Central Command] realized that it might have to conduct an evacuation from Mogadishu and was prepared to do that.

[17]: 84  The primary interest of the Ambassador was to maintain the US military's permission and access to airfields and ports in Mogadishu and Berbera, which the US had negotiated in 1979.

This was especially important given the mobilization for intervention in Kuwait, Somalia's strategic location near the Arabian Peninsula and the mouth of the Red Sea, and because Saudi Arabia would not allow US troops on their soil.

The embassy was also home to a large number of USAID staff, although the spread of unrest into the countryside was making their work increasingly difficult.

[17]: 86 The Somali Civil War spread through the country during 1990 and late in the year there was an increasing level of criminal violence in Mogadishu.

[20]: 9 [21] Ambassador Bishop had spent a considerable amount of time discussing contingency plans for evacuation with other diplomatic posts.

[20]: 2 On January 4, several incidents, including several exchanges of gunfire, suggested that the embassy's security detail was insufficient to hold off armed Somalis until USS Guam and USS Trenton arrived with their helicopters and soldiers, at that time scheduled to arrive on January 7.

[17]: 95  Ambassador Bishop made an urgent request to Washington for two platoons of soldiers to parachute into the embassy to defend it until the ships arrived.

[17]: 101–102 [20]: 34 [23] The United States has reopened its embassy in Mogadishu nearly three decades after Somalia collapsed into civil war on October 2, 2019.

The first US consuls in Mogadishu set up their initial office in a small room in the city's Public Works Department building.

[17]: 86  The grounds consisted of the Chancery, the Joint Administrative Office (JAO), Marine House (for the Marine Security Guards), the ambassador's residence, a building for the United States Information Service, an American school, a recreational complex for the local expatriate community, a 102-foot (31 m) water tower, and various storage and maintenance buildings.

[20]: 26  The ambassador's residence was largely constructed in glass, had no protective barriers, and its top story overlooked the embassy's walls.

[17]: 86 After the failure of UNOSOM in 1991–2, the US led a multinational mission—UNITAF—which included military forces to ensure aid was distributed to Somalis.

[26] The US military entered Mogadishu on December 9, 1992, and moved to quickly secure the abandoned embassy, along with the airport and port.

[27]: 97  The embassy complex itself was in disrepair; buildings had been stripped bare, a foot (0.3 m) of debris and trash covered the floors of the chancery, and bodies were found in some areas on the premises.

[19][35][36] He indicated that, although there was no set timetable for the premises' relaunch, the US government has begun upgrading its diplomatic representation in the country.

[35] President of Somalia Hassan Sheikh Mohamud and Prime Minister Omar Abdirashid Ali Sharmarke presented to Kerry the real estate deed for land reserved for the new US embassy compound.