Mateus Fernandes later became the primary architect of the next king, Manuel I of Portugal, who made him the supervisor of other architectural works in the rest of the country.
However, Mateus Fernandes is best known for his work in "Manueline style" at the entrance portal of the roofless, Unfinished Chapels (Capelas Imperfeitas) of the Monastery of Batalha.
The original plans for an octagonal dome, supported by buttresses, to crown this pantheon to the House of Aviz was never to be finished since funds ran out, and the construction of the Jerónimos Monastery at Belém would gain absolute priority.
Together with the architect Diogo Boitac, he rendered the Manueline style in the tracery of the arcade screens in the ambulatory of the Royal Cloister (Claustro Real) in the Jerónimos Monastery.
He (or his son, since they carried the same name) is reported to have directed the construction of the church and the hospital of Misericórdia at Óbidos, while they were engaged at the same time in Caldas da Rainha.