It was created by Philip II, a man who loved nature, and is a great location for reflection. This monastery is mentioned by Manuel Azaa, who attended the Augustinian friars' school there, in both his memoirs and the book El jardn de los frailes (The Friars' Garden). For the students, it serves as both a study and recreational space. The gardens belonged to the king, who saw them as a place to cultivate fruits, vegetables, and medicinal plants as well as a place of beauty with fountains and flowers. The monarch hired the best gardeners, both foreign and Spanish, and collected blueprints of gardens in France, Italy, England, and the Netherlands. This now-spartan garden was formerly covered in flowers, creating a kind of tapestry, and as a result it was compared to the carpets brought from Turkey or Damascus. Additionally, it was a true botanical garden with 400 plants imported from the New World, up to 68 different flower species, many of which were therapeutic.

The Convalescent Gallery or Corridor of the Sun, a sizable, light-filled area created for the sick to rest, is located to the southwest of the garden. Perhaps due to the requirement to ensure the monks' enclosure, it is supported by the tower of the apothecary. Contrasting with the more open façade facing the gardens, which is where the arched solution with arches above Ionic colonnades is unique in the monastery, is the sober façade facing the west.