There he studied till 15 July 1623, when he proceeded to Paris, took his degree as Doctor of Divinity, and was made a professor at the Sorbonne.
When Bishop Richard Smith fled from England in 1631, there arose a difference of opinion between the Jesuits and the other religious orders, who on the one hand thought the presence of a bishop in England was not advisable at the time, and the secular clergy, who took the opposite view.
In 1655, on the death of Bishop Smith, the question again arose, and Holden's friend and brother-priest, Thomas White, alias Blackloe, wrote a book, "The Grounds of Obedience and Government", which gave offence to his opponents, and led to some of his other works being censured by the Holy See.
The sisters were originally Franciscans, but when Cardinal de Retz, Archbishop of Paris, refused to allow Franciscans to dwell in his diocese, they obtained leave from the Holy See to change their rule to that of the Immaculate Conception of our Lady, and Dr. Holden was appointed their superior in 1661.
He also signed the Sorbonne's censure of Antoine Arnauld's letter to Roger du Plessis, duc de Liancourt.