Roman Catholicism is one of the primary sects of the Christian religion. The sect claims that its leader, the Pope, is the successor by an unbroken line of divinely-inspired selection tracing back to Jesus Christ's selection of the apostle Peter to be his successor as head of the church. The administrative center of the Roman Catholic Church is located on and around the Vatican plain in Rome, which today is a nominally autonomous nation. The principal religious ritual of the Roman Catholic Church is the Mass, continaing a ritual called the Eucharist in which the priest officiating over the ritual is said to transform the host, a wafer of bread, into the Body of Christ and a quantity of wine in a chalice, into the Blood of Christ, which are then dispensed to the congregation so as to commune with God.

The considerable administrative apparatus of the Roman Catholic Church built up over the centuries between its founding and the events in the Baroque Cycle have resulted in the Church amassing considerable wealth, political power, and serving as a repository for substantial amounts of education and knowledge, notably in the hands of an order within the Church known as the Society of Jesus or the Jesuits.

England first rejected Catholic rule under Henry VIII Tudor, who arrogated to himself several powers previously held by the Pope, particularly the appointment of bishops and the granting of divorces and annulments of marriages. This led to the creation of the Anglican Church, which eventually became the Established religion of England. Popular distrust of Catholics leads to the erosion of support for James II Stuart and makes the Glorious Revolution possible. Tension between Catholics and Protestants underlied the Thirty Years War, and serves as a pretext for the political struggles between William of Orange and Louis XIV which forms the backdrop for the political events depicted in the Baroque Cycle.

The Church as an institution does not play a large, direct role in the Baroque Cycle. However, the subtext of sectarian conflict within Christianity permeates the work, particularly with the disdain given to those sectarian differences by all three primary characters who each come to abhor the wars caused by these conflicts. Louis XIV casts himself as the defender of the Catholic faith and its foremost warrior; there is little doubt, however, that he has wrapped himself in the garments of the faith for purely self-serving purposes. Father Eduoard de Gex is the only Catholic cleric with any significant role in the Baroque Cycle, and he is a figure of evil, chaos, and irrationality. The only other Christian cleric depicted in the Cycle is John Wilkins, the Anglican Bishop of Chester, who is Daniel Waterhouse's early patron. The positive and warm depiction of Wilkins, however, seems to be based on his role as a Natural Philosopher and as a man who sees beyond the religious differences between himself and his protege and takes the true measure of the young man before him.