The organ of the church of São Domingos in Encarnação is, probably, the oldest extant instrument in the district of Mafra. According to the surviving documentation, it was constructed by the organ builder Bento Fontanes (son of João Fontanes de Maqueira) and bought by the brotherhood of Our Lady of the Incarnation, through its procurator, Father Isidoro Alves de Carvalho, for the amount of 235 thousand réis. The instrument was certified on 10 April 1770 by Brother José de Santa Ana, organist of the Royal Convent of Mafra.
Situated in the high choir of the church, it is a cabinet organ with a single keyboard of forty‐seven keys with a “short” first octave. This disposition of the first octave (see diagram) was much used in Portugal until the middle of the 18th century, being gradually abandoned in favour of the complete octave. This is the only keyboard of this kind extant in the district of Mafra. It has eight registers, of which four are full registers and two (Cornetilha and Voz humana) are half‐registers for the right hand. The stops that control the registers are situated to the right of the console, in the manner of the Italian organs of the period, which is a result of the strong Italian influence which made itself felt in Portugal from the beginning of the 18th century. Another indication of this Italianizing tendency is the presence of the Voz humana (an undulating flue stop found in Italian organs from the 17th century onwards, under the name Voce umana). These characteristics are common to other instruments by Bento Fontanes, such as the organ of the church of the Misericórdia in Torres Vedras.
The instrument survived until the present practically in its original state, being completely restored in 2004 by the organ builder Dinarte Machado.