Former Muslim guerrillas are now governing a poverty and conflict-wracked Muslim autonomous region under a peace deal partly aimed at combating ISIS-aligned militants in the southern Philippines.

Moro Islamic Liberation Front rebel chairman Murad Ebrahim assumed leadership on Tuesday in a ceremony in Cotabato city of an 80-member transition authority dominated by his guerrilla group to govern a five-province region called Bangsamoro.

The first large group of about 12,000 combatants is expected to be demobilised starting this year under the deal.

The Philippine and western governments and the guerrillas view effective Muslim autonomy as an antidote to nearly half a century of Muslim secessionist violence, which ISIS exploited to gain a foothold in the region.

“Our enemy during this struggle is not the soldiers. Our enemy is not the government,” Mr Murad said in a speech after taking leadership of the Bangsamoro Transition Authority as interim chief minister. He said he and his men would wage a new jihad, or holy war, against corruption and mismanagement.

“Our enemies are all the ills of governance in this system. Our enemies are graft and corruption. Our enemy is manipulation of government. Our enemy is nepotism,” said Mr Murad, who once led rebel forces in marshy battlefields that his group will now try to turn into progressive communities.

Mr Murad and his insurgent group inherit a region of more than 3.7 million people, nearly half of whom wallow in poverty. Many have been exposed to decades of violence and fighting, according to regional government reports prepared for the rebels-turned-officials.

Muslim militant groups including the Bangsamoro Islamic Freedom Fighters and the Abu Sayyaf continue to threaten the region, the reports said.

Bangsamoro replaces an existing poverty stricken autonomous region with a larger, better-funded and more powerful entity. An annual grant, which could reach more than $1 billion, is to be set aside to bolster development in a region with little infrastructure that is deeply scarred by decades of fighting.

“There is a daunting task ahead as we lay down the foundations of the Bangsamoro Autonomous Region in Muslim Mindanao,” presidential adviser Carlito Galvez said. “I’ll be frank, the transition process is difficult. But there is no challenge that we cannot surmount.”

Under the peace deal brokered by Malaysia, the rebels gave up their goal of a separate state in exchange for broader autonomy. The 40,000 fighters and at least 7,000 firearms that Mr Murad’s group has declared are to be demobilised in three phases, depending on progress in the agreement’s enforcement.

Mr Murad’s people, including fierce Muslim commanders still facing criminal cases for past attacks, are to comprise 41 of 80 regional administrators. President Rodrigo Duterte picked his representatives to fill the rest of the transition authority, which will also act as a regional parliament until regular officials are elected in 2022.

Members of another Muslim rebel group, the Moro National Liberation Front, which signed a 1996 autonomy deal that has largely been considered a failure, have also been given seats in the autonomous government.