The job will require a difficult balancing act that will be familiar ground to the retired four-star Marine officer, who has plenty of experience managing unwieldly coalitions and navigating the volatile politics of the Middle East.
Allen, 60, has been an unabashed hawk when it comes to Islamic State, urging a no holds-barred assault on the militants, who have employed brutal tactics in their advance across Syria and Iraq.
As head of the NATO-led mission in Afghanistan from July 2011 to December 2013, Allen had to deal with the notoriously mercurial president Hamid Karzai -- as well as commanders from dozens of countries while overseeing the start of a troop drawdown.
And before that, as the number two at US Central Command, which oversees American forces in the Middle East, Allen devoted much of his time to tracking America's arch-foe Iran.
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President Barack Obama, in announcing a strategy to destroy the group, said the creation of an international coalition that included Arab and Muslim states was vital to the anti-IS effort.
Allen's deputy will be Brett McGurk, the deputy assistant secretary of state for Iraq and Iran.
The former commander will not oversee military operations, which is the job of the current chief of Central Command, General Lloyd Austin. But Allen likely will be asking members of an international coalition to contribute aircraft, ammunition, access to bases or other aid to the fight.
The approach to the Sunni tribal leaders was controversial at the time, and some fellow officers opposed the effort but it proved successful, producing the so-called "Anbar Awakening.