The extraordinary collection of paintings housed in the Monastery was reorganized in the second half of the 20th century for the proper installation of the collection, as the works had been poorly exhibited since antiquity in the Chapter Rooms and in the Sacristy, where the limited and inappropriate lighting and lack of space not only made it difficult to contemplate the paintings but also diminished their superb quality of colors, light, and composition.

In this regard, the main focus was on giving the commemoration of the Monastery's fourth century of construction the maximum significance and effectiveness. One of the most notable restoration projects was the work done on Philip II's Summer Palace, which was in utter disrepair with no carpentry, no soldiers, and damaged plastering. Paintings from the Flemish, German, Italian, and Spanish schools have been installed in these rooms, which are on the ground floor, at the level of the Jardn de los Frailes (Friars' Garden), and include all the halls and chambers with their saloons, which coincide exactly with those of the upper floor or Palace of Philip II and which surround the Patio de los Mascarones. When all the additions were removed and the original structure was rebuilt, the halls, main rooms, and reception rooms that were added to this ensemble during the time of the founder were once again seen as they were intended, with dimensions and an appearance similar to the Chapter Rooms, but they were divided in height and abundantly partitioned during the time of Charles IV. Ten rooms in total have given Madrid access to a new significant international art exhibition.

German and Flemish schools produced paintings in the 15th and 16th centuries in Room I. The most significant pieces in this exhibit include Patinir's Landscape with Saint Christopher, Bosch's The Improper Puppets (Ecce Homo), a portion of The Creation, a recreation of The Garden of Earthly Delights, Dürer's Studies in Natural History, and a Triptych by Gerard David with The Pieta (center), Saint John the Baptist (left), and Saint Francis Receiving the Stigmata (right). Along with The Temptations of Saint Anthony from the school of Bosch, The Moneychanger and His Wife by Marinus Reymerswaele, Rest on the Flight into Egypt, credited to Quentin Massys, and a sizable Gothic Calvary cloth painted rather than embroidered in the 15th century using the "trepas or repostero" technique are other notable works of art.

Michel Coxcie, a Flemish artist, created the Triptych of St. Philip, the Annunciation, the Madonna and Child with St. Joseph and St. Anne, the Madonna and St. Joseph prostrating before the Child Jesus, the Offering to the Child Jesus, and the Holy Supper in Room II.

The Burial of Christ, Christ Crucified, whose Redeeming Blood is Collected by Three Angels, Christ Shown to the People by Pilate (Ecce Homo), The Prayer in the Garden, and St. Jerome in Prayer are among the valuable Titian works found in Room III. The Adoration of the Kings and The Rest during the Flight into Egypt by Francesco Bassano, as well as Noli me tángere, a replica of the Veronese by Luca Giordano, are also on show.

The expansive Room IV, which corresponds to the Throne Room on the ground floor, features, among other things, artwork by Titian (The Last Supper and St. John the Baptist), a superb series by Tintoretto (The Magdalene Anointing the Feet of the Lord in the Pharisee's House; Penitent Magdalene; The Burial of Christ; Fainting of Queen Esther Before Ahasuerus and Nativity with the Adoration of the Shepherd (Adoration of the Kings and Adoration of the Shepherds).

Three of José de Ribera's works, including Saint Jerome the Penitent, Saint Anthony, Joseph Shepherding Laban's Cattle, Saint Francis, The Burial of Christ, The Hermit King, Saint Paul, The Philosopher Chrysippus, Saint John the Baptist as a Child, and Aesop, are featured in Room V, which is devoted to his works.

Different Talavera ceramic models, made for the needs of the Monastery, are on display between Rooms V and VI in an open-plan cupboard on both sides with glass doors. These models include inkwells, jugs, plates, bowls, platters, dishes, slings, basins, tiles for plinths and shelves, and tiles for angled surfaces.

The Tunic by José de Velázquez, painted during the Sevillian artist's sojourn in Rome in 1630 (like The Forge of Vulcan) stands out among the works from the Spanish school of the 17th century in Room VI, which corresponds to Philip II's chambers on the upper level. Other noteworthy works are Presentation of the Virgin in the Temple by Zurbarán, Birth of the Virgin by Valdés Leal, Virgin and Child by Alonso Cano, View of the Palace of Aceca by Juan Bautista del Mazo, and a Portrait of Charles II as a Child by Carreo de Miranda.

Alessandro Bonvicino "Morettomasterpieces "'s The Prophet Isaiah and the Eritrean Sibyl, Mariotto Albertinelli's Mystical Subject, two anonymous grisaille paintings (Descent of Christ into Limbo and Resurrection and Virgin and Child), and Saint John the Baptist, a copy of Raphael by Nicolas Poussin are just a few of the notable Italian school paintings found in Room VII.

A few other pieces from the Italian school can be found in Room VIII, including Descent from the School of Veronese, Lot intoxicated by his Daughters, by Guercino, Madonna and Child, Saint John Child (The Virgin of the Oak Tree), attributed to Pordenone, and an Ecce Homo by Giovanni Battista Crespi.

Various artworks from the Italian, Flemish, and Dutch schools can be seen in Room IX. These include paintings by Rubens, Daniel Seghers, Van Dyck, and Jan Davidsz de Heem (Virgin and Child, Still Life with Pomegranates, Pears, and Grapes, and Still Life with Grapes, Pears, Pears, Plums, and Apples Being Pecked by Birds), as well as Daniel Seghers and Daniel Seghers (The Supper at Emmaus, a sketch of the painting now in the Prado).

The Martyrdom of Saint Maurice and the Theban Legion by El Greco, The Calvary by Van der Weyden, a magnificent replica of the Descent from the Cross by Michel Coxcie (the original is on display in the Prado), and a stunning tapestry from the series of The Conquest of Tunis, a significant piece by the Brussels master Willem Pannemaker created in the middle of the 16th century, are among the extraordinary works that are housed in two large vaulted

The Adoration in the Name of Jesus (also known as The Dream of Philip II), Saint Eugene, and Saint Peter are among the paintings by the Cretan artist on exhibit in Room X, which is also known as the Sala de los Grecos. A stunning Flemish tapestry from the 16th-century series The Spheres is on show along with two pieces by Carletto Veronese, both of which are depictions of The Adoration of the Kings.