Im März 1644 war Elisabeth von Bourbon noch einmal schwanger geworden, aber sie verlor das Kind (Fehlgeburt) und wurde krank. Ihr Gatte war in dieser schwierigen Zeit in Aragon, um den Krieg gegen die Franzosen zu organisieren. "Philip was still rejoicing over the capture of the important city of Lerida at the middle of August 1644, and the relief of Tattagona in September, when ill news came to him of his wife's health. ... Messengers were sent to the King, whilst the doctors, as was their wont, bled the patient copiously until they had left her bloodless, thought with symptoms which now would be recognised at once as those of diphtheria. Then, in their desperation, the dead body of St. Isidore the Husbandman and the sainted image of the Atocha were brought to the palace; though the dying woman protested that she was unworthy to have them brought to her bedside. But the inflammation of the throat increased, notwithstanding all the charms of the Church and the prayers of young Baltasar Carlos [her son], who was devotedly attached to his mother. There was no church nor convent in Madrid that did not bring out in procession its crucifixes and most sacred images in prayer for the Queen's restoration to health ... On the 5th October the Queen tried to make a new will, but she was too weak to sign it, and only left verbal testamentary instructions before witnesses for the King to be informed of her wishes. At noon that day she sent for a fleur de lys which formed one of the ornaments of the crown, and in which there was a fragment of the true Cross. This she worshipped fervently, and her two children, Baltasar Carlos and Maria Teresa, were brought to her; but she would not suffer them to approach her for fear of infection, though she blessed them fervently from a distance. The next day, at a quarter past four in the afternoon, stout-hearted loyal Isabel of Bourbon breathed her last, aged 41." (in: Martin Hume: The Court of Philip IV. - Spain in Decadence, id., pp. 392-393).
Philipp IV. schrieb an die Äbtissin Maria von Agreda anlässlich des Todes seiner Gattin Folgendes: "I find myself in the most oppressed state of sorrow possible ... for I have lost in one person everything that can be lost in this world; and if I did not know, according to the faith that I profess, that the Lord disposes for us what is best, I do not know what would become of me." (in: Martin Hume: The Court of Philip IV. - Spain in Decadence, id., p. 395).