The museum preserves an important group of paintings by the Cretan painter, all of them of excellent quality and set at his final phase between 1600 and 1614. Among them we highlight the View and Plane of Toledo, the Apostolate serie, the protraits of Antonio and Diego de Covarrubias, and the altarpiece of Saint Bernard.

The Tears of Saint Peter, dated between 1587 and 1596, is also a remarcable painting, and is considered the best version of this specific topic.

Along with El Greco's paintings the museum exhibits works from Luis Tristan, his best disciple, his son Jorge Manuel, and other painters of the time from Toledo, as well as paintings of the schools of Madrid and Seville in the 17th century. These works are complemented by the adquisitions of the marquis that can be seen in the Room "Museum of Spanish Art".