After its abandonment, Queen Maria II was asked to bequeath the church of the Monastery to the people of Batalha due to the dilapidated state of the parish church, to which she acquiesced. The old monastic church has since been used to celebrate the Dominican mass and holy days, as well as weddings, to this very day.
During the 1940s, as would be the case more or less all over the country, the desire to return this place of worship to its alleged original gothic purity was in vogue, stripping the 16th, 17th and 18th century alterpieces from its apse and transept chapels. The General Directorate for Buildings and National Monuments took it upon itself to disassemble these altarpieces and reassemble them in other places of worship. For example, the 16th century altarpiece of the Chapel of Saint Miguel, the pantheon of the Counts of Miranda, next to the doorway of the transept, was transferred to the main chapel of the parish church of Batalha.
By the same token, a monumental neogothic baptistry that had been installed to the left of the main entrance here was disassembled and placed in the church of Our Lady of Remedies, in Reguengo do Fetal.
In keeping with contemporary liturgical tastes, as was agreed during the second session of the Second Vatican Council in 1963, the high altar was subsequently transferred from the interior of the main chapel to the crossing of the monastic church.