In exchange for freedom, the government persuaded them to turn themselves in -- a move aimed at ending an insurgency by Boko Haram and the Islamic State West Africa Province (ISWAP) group that has killed thousands and displaced over two million more since 2009.
But an investigation by AFP points to major failings in the screening and deradicalization process, while the need for justice has been set aside.
In May 2021, a key event gave the authorities an opportunity.
Boko Haram leader Abubakar Shekau died after rivals ISWAP invaded his hideout demanding he pledge allegiance.
After his death, his fighters and their captives had a decision to make: either join ISWAP or flee.
More than 90,000 people formerly associated with Boko Haram and, to a much lesser extent, ISWAP defected.
Most have transited through Hajj and some through Shokari or Bulumkutu, which are similar centers.
The large majority of those who turned themselves in are not former fighters but rather men, women and children who lived under jihadist rule. Even so, the centres' potential to usher in peace has attracted global attention.
The European Union, Britain and the United Nations are all in favor of the initiative - known as the Borno Model - and pledged to support the expansion of a program presented to them as a way to help end conflicts.
Official documentation says the scheme takes far-reaching steps to separate former fighters from non-combatants -- an "intensive process of identification and evaluation."
But the former residents, whose names have been changed for the purpose of this article, all described the screening system as threadbare.
Among the three former fighters interviewed by AFP, only one said he was asked which battles he had participated in and why.
Two women said they had not been asked any questions at all - and that females were simply categorized as "wives."
In theory, non-combatants stay only a couple of days or weeks in the centers, while former fighters are kept for several months. Certain camp residents get day passes to roam freely in the city.
Interviewees told AFP that some are released more quickly than others, either to make space for new arrivals or because community leaders give them authorization to leave.
An official said former fighters are given a two-week training course that includes classes on "values in Islam", "fundamental human rights" and basic civic education.
Before they are released, the men also have to take an oath, swearing on the Koran that they will not go back to the bush or spy for those still fighting.
Momo, who joined Boko Haram when he was 13, told AFP he had taken part in "many attacks" against soldiers and "disbelievers" to establish "an Islamic state" before deciding to surrender.
During his five months in Hajj, the now 26-year-old said preachers advised him and others to "be patient with people when we leave, that we have to be obedient with local authorities and that we should be serious about our religious duties."
That was the extent of the "deradicalization" process he said he went through.
An additional motivating factor for those in the armed groups is that once they surrender, the authorities give them money - monthly stipends and a lump sum when they leave - as well as food and other basic goods.
But this stirs resentment among residents of Borno who have suffered from the conflict.
And while security experts insist on the value of providing an exit path to those who want to surrender, many believe that victims also deserve some redress.
"Serious crimes have been committed... Someone must be held to account, because without some measure of justice, it's hard to see how there can be lasting peace," said an international security expert in the country who asked to remain anonymous.