Some experts have warned that the withdrawal of an estimated 700 US military personnel comes at the worst possible time for Somalia, as the al-Qaida-linked al-Shabab extremist group improves its bomb-making skills and continues to attack military and civilian targets, even in the capital Mogadishu.
The withdrawal comes less than a month before Somalia is set to hold a national election.
The US personnel trained and supported Somali forces, including its elite special forces, in counter-terror operations.
They are being moved to other African countries such as neighbouring Kenya and Djibouti, home to the only permanent US military base in Africa, but US Africa Command spokesman Colonel Chris Karns would not say how many were going where.
Asked whether the administration of President-elect Joe Biden would reverse the withdrawal, Col Karns replied in an email: "It would be inappropriate for us to speculate or engage in hypotheticals."
Col Karns said the operation enters its "next phase of periodic engagement with Somali security forces" but would not go into details.
The withdrawal was announced late last year, with a January 15 deadline.
The US military, which has carried out a growing number of airstrikes against al-Shabab and a small band of fighters linked to the Islamic State group during Trump's administration, says it will continue to pressure al-Shabab.
The extremist group has an estimated 5,000 to 10,000 fighters.
Those Somali forces, even US assessments have said, are not ready to take over responsibility for the country's security, especially as a 19,000-strong multinational African Union force is also set to withdraw by the end of this year.
The US Africa Command commander, General Stephen Townsend, noted "no serious injuries or significant loss of equipment, despite significant efforts to target us by al-Shabab" during the "intense" operation to remove the US personnel.