The sacristy dates back to 1622 and is of mannerist architecture, designed by Pedro Tinoco. The Sacristy of the Santa Cruz Monastery is perhaps the largest in Portugal. The huge window above gives an extraordinary brightness, as do the extraordinary octagonal boxes that fill the vaulted ceiling and the two-tone stone floor.

Here you can see the chest made of exotic wood from Brazil and decorated with ivory, dating back to the 17th century, and also the amurio wardrobe, set in the east wall, which bears the emblematic Cross supported by two angels, and where they are still found some ivory plates identifying the names of some of the last Crúzios users (the name by which the friars of the monastery were known).

On the walls covered with 17th century tiles, there are panel paintings from the beginning of the 16th century: "O Pentecost" by Grão Vasco, "Ecce Homo" and "O Calvário", the Virgin and the "Holy Women" by Cristóvão de Figueiredo, two of the best painters of the 16th century. Also magnificent is "The Descent from the Cross", an 18th century painting attributed to André Gonçalves. There are also paintings by Garcia Fernandes.

There are also large wooden sculptures from the 17th century: the Crucifixion with Christ, the Virgin and Saint John, and also Saint Gudula and Saint Gertrude, two saints of the Augustinian Order.

On the east side of the sacristy is the 17th century tile-covered vaulted sink.