It is unknown whether Zurbarán had the opportunity to copy the paintings of Michelangelo da Caravaggio; at any rate, he adopted Caravaggio's realistic use of chiaroscuro. The painter who may have had the greatest influence on his characteristically severe compositions was Juan Sánchez Cotán. Polychrome sculpture — which by the time of Zurbarán's apprenticeship had reached a level of sophistication in Seville that surpassed that of the local painters — provided another important stylistic model for the young artist; the work of Juan Martínez Montañés is especially close to Zurbarán's in spirit.

He painted directly from nature, and he made great use of the lay-figure in the study of draperies, in which he was particularly proficient. He had a special gift for white draperies; as a consequence, the houses of the white robed Carthusians are abundant in his paintings. To these rigid methods, Zurbarán is said to have adhered throughout his career, which was prosperous, wholly confined to Spain, and varied by few incidents beyond those of his daily labour. His subjects were mostly severe and ascetic religious vigils, the spirit chastising the flesh into subjection, the compositions often reduced to a single figure. The style is more reserved and chastened than Caravaggio's, the tone of color often quite bluish. Exceptional effects are attained by the precisely finished foregrounds, massed out largely in light and shade.

While in Seville, Zurbarán married Leonor de Jordera, by whom he had several children. Towards 1630 he was appointed painter to Philip IV; and there is a story that on one occasion the sovereign laid his hand on the artist's shoulder, saying "Painter to the king, king of painters." After 1640 his austere, harsh, hard edged style was unfavorably compared to the sentimental religiosity of Murillo and Zurbarán's reputation declined. It was only in 1658, late in Zurbarán's life that he moved to Madrid in search of work and renewed his contact with Velázquez. Zurbarán died in poverty and obscurity.

In 1627 he painted the great altarpiece of St. Thomas Aquinas, now in the Seville museum; it was executed for the church of the college of that saint there. This is Zurbarán's largest composition, containing figures of Christ, the Madonna, various saints, Charles V with knights, and Archbishop Deza (founder of the college) with monks and servitors, all the principal personages being more than life-size. It had been preceded by numerous pictures of the screen of St. Peter Nolasco in the cathedral.

In Santa Maria de Guadalupe he painted various large pictures, eight of which relate to the history of St. Jerome; and in the church of Saint Paul, Seville, a famous figure of the Crucified Saviour, in grisaille, creating an illusion of marble. In 1633 he finished the paintings of the high altar of the Carthusians in Jerez. In the palace of Buenretiro, Madrid, are four large canvases representing the Labours of Hercules, an unusual instance of non-Christian subjects from the hand of Zurbarán. A fine example of his work is in the National Gallery, London: a whole length, life-sized figure of a kneeling Franciscan holding a skull. His principal scholars were Bernabe de Ayala and the brothers Polanco (painters).

In 1756 Richard Trevor who was Bishop of Durham from 1752 to 1771 bought a series of 12 of the 13 portraits of Jacob and his 12 sons and these are still in Auckland Castle, Bishop Auckland, near Durham, England. The paintings were on a ship that was seized at sea and were then sold to the bishop for £125. The portrait of Benjamin was sold separately to the Duke of Ancaster and hangs in Grimsthorpe Castle, Lincs. The bishop had to be content with a copy by Arthur Proud.

In 2001, the Church Commissioners voted to sell the paintings which have a £20m valuation, but relented until a review in 2010.