There were celebrations last weekend when the two sides signed the deal paving the way for civilian rule.
The sovereign council that will oversee Sudan's transition to democracy is due to take office in the next few hours.
Generals and protest leaders agreed on its final composition on Tuesday, four months after Sudan's long time ruler, Omar al-Bashir, was forced out of power.
The council consists of five military officers and six civilians - two of them women, one from Sudan's Christian minority.
Among those being sworn in is the outgoing military leader, Lt-Gen Abdel Fattah Abdelrahman Burhan.
He will be in charge of the sovereign council for the first 21 months; a civilian will then take over until elections in 2022.