Morales was a painter with a highly individual style; his meticulous technique and the prominent echoes of the styles and forms of Leonardo da Vinci and Raphael indicate the formative influence of Italianizing Flemish painters. This would seem to confirm Palomino's statement that Morales trained in Seville with the Flemish Mannerist, Peeter de Kempeneer (Pedro de Campaña), who is recorded in Spain from 1537 (see A.A. Palomino de Castro y Velasco, Museo pictórico [1712-24], III, trans. N. Alaya Mallory, as Lives of the Eminent Spanish Painters and Sculptors, Cambridge, 1987, p. 38). Morales' earliest dated work, the Virgin with the Little Bird now in a private collection, Madrid, dates from 1546. His only signed work is the Raphaelesque Madonna of Purity in San Pietro Maggiore, Naples.
Morales' oeuvre was exclusively religious in subject matter, concentrating on the imagery of the Passion, and reflects the preferred subjects of meditation of contemporary Spanish mystics such as Saint Peter of Alcantará (1499-1562), Fray Luis de Granada (1504-1588) and Juan de Avila (1500-1569). Numerous replicas and versions of these subjects testify to their enormous popularity as images of devotion, and Ecce Homo was a subject that Morales repeated several times. The closest seems to be that recorded on a Witt photograph mount as in the collection of Pr. Kotchoubey, although in the latter there are minor differences in the position of the stick that Christ holds.