[8] Following the United States invasion of Afghanistan, Zakir surrendered to US forces and was interned in the US Guantanamo Bay detention camp in Cuba.

The school was affiliated with an Afghan mujahideen group under the command of Mohammad Nabi Mohammadi that was fighting against the Soviets in Afghanistan.

[4] During the Afghan civil war, Nematullah was killed in a fight against then warlord and later politician Ismail Khan in Herat province and Zakir took command of his group.

[9] He was named "Mullah Y Abdhullah" on the Summary of Evidence memo prepared for his 2007 annual Administrative Review Board.

[4][13] Patrick Mercer, a member of the United Kingdom Parliament and its counter-terrorism subcommittee, expressed surprise that he had been allowed to rejoin the Taliban, wanting to know why he had been released.

[5] He was living in Quetta and had command of the four southern provinces of Helmand, Kandahar, Uruzgan and Zabul, with the power to appoint Taliban governors there.

Anand Gopal reported that Zakir helped write a Taliban "rule book" that sought to limit civilian casualties.

[10] On March 1, 2010, The News International reported that Zakir was part of the Taliban's Quetta Shura, and that he had been arrested by Pakistani authorities in recent raids along with nine other leaders, the most senior of whom was Abdul Ghani Baradar.

[4] On March 4, 2010, the Associated Press reported "two senior Afghan intelligence officials" claimed Abdullah Ghulam Rasoul had emerged to be a senior Taliban leader, and that he was under consideration to replace Abdul Ghani Baradar as number two in the Taliban's chain of command, following Baradar's arrest.

[18] The Wall Street Journal reported in April 2014 that Zakir had left the position of chief military commander.

Some informants said that he was demoted, because of his strong opposition to peace talks with the Afghan Government and disagreements with more moderate leaders such as Akhtar Mansour.