The lower cloister of the monastery is covered with a flat wooden roof called an alfarje with its exposed structure. It is made up of a succession of main beams or girders, which rest on the inner wall and on the outer wall of the cloister, and less square transversal beams or girders, between which wooden planks are placed. The entire structure in Silos is painted and some parts (the underside of beams and planks) are also carved with geometric motifs. The painted scenes that cover the main beams, the tabicas (boards placed between the gaps left by the intersecting tracks), the planks above them and those that join the walls constitute a catalogue of more than 600 representations of religious and profane themes, the latter being dominated by scenes of everyday life, with chivalric and amorous themes. It has been argued that the source for the production of these scenes is possibly The Book of Good Love by the Archpriest of Hita – written ca. 1330-1343 – which contains a wide collection of narratives and poetic compositions: fables, exempla and moralities, allegories, songs of the blind and profane and religious lyrical poems.

The coats of arms of the benefactors of the monastery at this time are painted repeatedly on the boards between the cross beams: the Castilian King Juan I (a lion on a white background, a castle on a red background), the Bishop of Burgos, Gonzalo Mena y Roelas (five gold stars on a blue field of the Menas and eight silver roundels on a red field of the second lineage) and another coat of arms consisting of a tree surrounded by a fleur-de-lis border.

The scenes and iconographic motifs are depicted on the faces of the main beams and on the aliceres – ceramic friezes – on the walls. They are framed in combined arches, formed by a border decorated with white ovals with red pearls. The vegetal motifs complete the sides of the scenes, with carved rosettes completing the partitions.

Some of the depictions are made to be viewed individually, but others form a continuous scene in the different vignettes sheltered by the combined arches along a beam. Two outstanding examples are the representation of the Adoration of the Magi and the representation of the parody of the Canonical Hours from the Book of Good Love featuring scenes of the wolf and the donkey, with a critical character and a moralising purpose. In addition to religious representations, such as the Gozos de Santa María (the “Joy of Saint Mary”), there are depictions of trotaconventos or matchmakers, amorous young people, monks and nuns from different orders, musicians with different instruments, knights and hunters, harpies, tradespeople such as the spinner woman, warriors with swords on horseback or on foot with crossbows and representations of bullfighting with confrontations with a bull on foot or on horseback.

Despite the apparent unity of the panelled ceiling, its execution was carried out in several stages and by several artists. The oldest parts are catalogued between 1366 and 1384 and are located in the north and west galleries of the cloister. Their figurative decoration is meticulous and well-proportioned. In 1384, the monastery suffered a fire and part of this panelled ceiling had to be rebuilt. The south gallery dates from this time, with differences in the way it depicts trees, animals, family coats of arms and other decorative details. The entire east gallery and part of the north gallery were rebuilt between 1888 and 1890, when the French monks dismantled the entire ceiling to tie up the cloister walls and prevent their collapse and ruin. All the ends of the beams have a T-shaped plate attached with three screws and the head of the plate is inserted into both walls, thus acting as braces. Several panels painted at the end of the 15th century, which may have been in the chapter hall, have also been embedded in some of the north gallery’s finishes.