In the Chancel, special emphasis is placed on the tomb compositions of the first two kings of Portugal: D. Afonso Henriques at the Gospel (left side of the altar) and his son D. Sancho I at the Epistle (right side of the altar).

The two tombs are included in a magnificent sculptural work by the French sculptor Nicolau de Chanterene.

The construction of the tombs, where the first two kings of Portugal are located, dates back to 1520, with Gothic architecture with Renaissance and Manueline elements. It was at this time that King D. Manuel I ordered the transfer of the mortal remains of D. Afonso Henriques and D. Sancho I from the tomb chests that were located in the central body of the Church to the Main Chapel. The transfer of the mortal remains of the two kings took place in 1531.

On the Gospel (left side of the Altar) lies a tomb with the title D. Afonso Henriques, the founder of the Kingdom of Portugal. The tomb is surrounded by large altarpieces with statues of Saints – in the upper central part we can see the Shield of Portugal supported by angels and in the side niches there are figures of Saint Christopher and Saint Helena.

In the lower central part, below is Our Lady of the Assumption, flanked by Angels and the Evangelists, St. Mark and St. Luke, on the flanks are faceted pilasters decorated with medallions, niches and statues of the 12 Apostles.

The Epistle (right side of the Altar) lies on top of the tomb with the title D. Sancho I (second King of Portugal and son of D. Afonso Henriques). As in the Tomb of D. Afonso Henriques, in the upper central part there is a sculpture of the Shield of Portugal supported by angels and flanked by Saint John the Baptist and Emperor Heraclitus or Constantine.

The tomb is surrounded by large altarpieces with statuary of Saints – in the lower central part there are images of Our Lady of Milk, Saint Catherine and Saint Magdalene and the Evangelists, S. Matthew and S. Luke, on the flanks they are found. faceted pilasters decorated with medallions, niches and statues – of the 4 doctors of the church, the 4 Cardinal Virtues (Justice, Fortress, Temperance and Prudence) and also the 3 Theological Virtues (Faith, Hope and Charity).

From the profuse decoration of the two tombs, it is worth highlighting the symbols of D. Manuel I – Armillary Sphere, the Cross of Christ and the Royal Symbol – which affirm and reinforce the charisma of D. Manuel I's royal power.

It is also worth highlighting, in this magnificent chancel, «The “portals” that lead the first two kings to the mythical sphere of the sacred by the enlightened hand of King D. Manuel, “enlightened” by the reason that legitimizes his power, find a clear parallel in the most paradigmatic work of his reign: the Jerónimos Monastery.”