In 1993 an assault force of Delta Force commandos backed up by nearly 140 United States Army Rangers and four US Army Special Forces operators under the command of Gen. William Garrison and Col. Lee Van Arsdale captured Qeybdiid together with Osman Ali Atto. He stayed in American custody for some months. The arrest is portrayed in the film Black Hawk Down.
By 2001, he was the chief of police over Mogadishu as part of the new Transitional National Government (TNG).
In 2006, he fought with the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT) against the Islamic Courts Union in the Second Battle of Mogadishu. They surrendered on 11 July, 2006, the last Alliance forces to do so.
In late 2006, after retreating from Mogadishu, he fought under the name of the newly-formed autonomous region known as Galmudug but with out any known affiliation or permission as yet. He led its forces, fighting alongside Ethiopia and Puntland allies, in the Battle of Bandiradley.
In October 2005 the Swedish newspaper Svenska Dagbladet reported that a video recording incriminating Qeybdid had circulated amongst politically active exiled Somalis for a long time. The film showed how the police chief participated in the execution of young boys in the Somalian town of Kismayo in 1991, the year of the overthrow of Siad Barre. The sequence is described as brutal, showing someone allegedly looking like Qeybdid interrogating a group of captured child soldiers before giving his militamen orders to open fire on them and kill them. Other claims related to his role in the militia of Mohamed Farrah Aidid in 1993, the time of the (first) Battle of Mogadishu.
The Swedish authorities' attempts to interrogate Qeybdid proved fruitless, as he refused to answer questions on the grounds that the interpreter provided for him was a member of an enemy clan. The defence attorney appointed to him said, however, that he maintained his innocence. Its well known that the murder of Swedish journalist Martin Adler in Mogadishu have been carried out by his followers in retaliation for this arrest.