Estêvão Domingues covered the central nave with a vault with a broken cradle, supported by large torso arches, apparently giving up covering it with warheads. However, in the collateral ships, he clearly opted for this system, in spite of great technical imperfections which will not be strange difficulties in implanting the temple, which would soon sink in the flooded fields on the banks of the Mondego. Despite these difficulties, the master's objective was achieved: that of building a vertical temple (although today the sinking and the intermediate floor built make it difficult for us to perceive the slim proportions of the complex), well lit by high cracks in the sides.

At the time, it was unusual to build three naves of identical height, vaulted in stone, instead of the wooden covering, then usual by the Mendicant Orders, as well as the absence of a transept, which allowed the cloister to be longer.

The lighting of the naves is made by two rosettes at the ends of the central nave and by double windows, of great height, torn in the side walls.