The Church, however, did not have a chancel. The construction of the chancel implied the thinning of the rocky massif on the hill of Vitória. Only in 1584 did Manuel Luís be called Amarante (where he was master of works in 1581-1584 at the Convento de S. Gonçalo) to build it, an enterprise sponsored by the legacy left by D.Lopo de Almeida, who died that year in Madrid. This chancel is inspired by the chancel of the Jerónimos Monastery of Jerónimo Ruão (1567-1572) son of João de Ruão. A semi-circular stone altarpiece surrounded by an apse and the overlapping of orders on the interior elevations. The chancel was built between 1584 and 1590