James's time in France had exposed him to the beliefs and ceremonies of Catholicism; he and his wife, Anne, became drawn to that faith.[32] James took Eucharist in the Roman Catholic Church in 1668 or 1669, although his conversion was kept secret for some time and he continued to attend Anglican services until 1676.[33] In spite of his conversion, James continued to associate primarily with Anglicans, including John Churchill and George Legge, as well as French Protestants, such as Louis de Duras, the Earl of Feversham.[34] Growing fears of Catholic influence at court led the English Parliament to introduce a new Test Act in 1673.[35] Under this Act, all civil and military officials were required to take an oath (in which they were required not only to disavow the doctrine of transubstantiation, but also denounce certain practices of the Catholic Church as superstitious and idolatrous) and to receive the Eucharist under the auspices of the Church of England.[36] James refused to perform either action, instead choosing to relinquish the post of Lord High Admiral. His conversion to Catholicism was thereby made public.[35] Charles II opposed the conversion, ordering that James's daughters, Mary and Anne, be raised as Protestants.[37] Nevertheless, he allowed James to marry the Catholic Mary of Modena, a fifteen-year-old Italian princess.[38] James and Mary were married by proxy in a Catholic ceremony on 20 September 1673.[39] On 21 November, Mary arrived in England and Nathaniel Crew, Bishop of Oxford, performed a brief Anglican service that did little more than recognise the Catholic marriage.[40] Many of the British people, distrustful of Catholicism, regarded the new Duchess of York as an agent of the Pope.[41]

In France, James was allowed to live in the royal château of Saint-Germain-en-Laye.[121] James's wife and some of his supporters fled with him, including the Earl of Melfort; most, but not all, were Roman Catholic.[122] In 1692, James's last child, Louisa Maria Teresa, was born.[123] Some supporters in England attempted to restore James to the throne by assassinating William III in 1696, but the plot failed and the backlash made James's cause less popular.[124] Louis XIV's offer to have James elected King of Poland in the same year was rejected, for James feared that acceptance of the Polish crown might (in the minds of the English people) render him incapable of being King of England. After Louis concluded peace with William in 1697, he ceased to offer much in the way of assistance to James.[125] During his last years, James lived as an austere penitent.[126] He wrote a memorandum for his son advising him on how to govern England, specifying that Catholics should possess one Secretary of State, one Commissioner of the Treasury, the Secretary at War, with the majority of the officers in the army.[127] He died of a brain hemorrhage on 16 September 1701 at Saint-Germain-en-Laye.[128] His body was laid to rest in a coffin at the Chapel of Saint Edmund in the Church of the English Benedictines in the Rue St. Jacques in Paris, with a funeral oration by Henri-Emmanuel de Roquette.[128] James was not buried, but put in one of the side chapels. Lights were kept burning round his coffin until the French Revolution. In 1734, the Archbishop of Paris heard evidence to support James's canonization, but nothing came of it.[128] During the French Revolution, James's tomb was raided.[129] At the time of his death, he was the last surviving child of Charles I and Queen Henrietta Maria.