The church interior is spacious with octagonal piers richly decorated with reliefs, and outside is a garden laid out in 1940 consisting of hedges cut in the shape of various municipal coats of arms of Portugal. In the center is a large fountain also decorated with coats of arms, often illuminated on special occasions.

In 1496, King D. Manuel I asked the Holy Sé for permission to build a large monastery on the banks of the river Tagus. The works started in 1501 and almost a century later everything was done. D. Manuel I and his descendants were buried in marble tombs located in the chancel of the church and in the transept lateral chapels.

Dedicating the monastery to the Belém Virgin was another factor that influenced the royal decision. The Jerónimos Monastery replaced the church of Saint Mary of Belém where monks of the Christ Order gave assistance to sailors passing through. For this reason, D. Manuel I chose the monks of the Saint Jerónimo Order whose functions were to pray for the soul of the king and give spiritual assistance to the sailors that left Praia do Restelo in discovery of new lands.

Because the monastery was built on the sand banks of the river Tagus, the great earthquake of 1755 had little effect on the structure.