The article presents the history of the Catholic churches, operating in Malbork in the early modern period. Most attention was paid to the parish St. John the Evangelist, which – with short breaks in the second half of the sixteenth century and during the First Swedish-Polish War – remained in the hands of Catholics. With post-visit protocols learn about repairs carried out, the order of worship and involvement of the clergy. On the basis of the preserved since 1700 year vital records we can conclude that each year about 200 children was baptized and was contained from 50 to 150 weddings. Since the second half of the eighteenth century there are also records of marriages concluded by Lutherans in the Catholic Church, even when both spouses were not Catholics.Apart from the parish of St. John the Evangelist churches still functioning: the castle of the Blessed Virgin Mary, St. Lawrence and the hospital of the Holy Spirit and Chapels.A major role in the pastoral care in the modern era played the Jesuits, who have taken the ministry in 1618.