The siege of Den Bosch was begun on april 30, 1629 the siege and the conquest of the city by the forces of the Dutch Republic under the leadership of Frederick Henry, Prince of Orange, the city and the surrounding area were seperated of the old Duchy Brabant. After a siege that lasted about four and a half months, Frederick Henry enters the city with his troops on September 17th.
Two days later, the first reformed service takes place in the Sint-Jan in presence of Frederick Henry and his wife Amalia of Solms-Braunfels. It is the beginning of a great turning point in the history of the city and the cathedral. A century and a half the Bosch people were denied the right to self-government and representation in the States General. Free exercise of the Catholic religion was abolished in 1629 and all male clergy had to leave the city within two months.
The church property was confiscated by the States General with the exception of the ecclesiastical ornaments that the expelled clergy were granted to keep. From 1629 until 1813, the Sint-Jan served as house of prayer for the Dutch Reformed congregation. About a fifth of the population was Protestant in this period, the rest remained Catholic and had to rely on conventicles for the exercise of their religion.
After the capitulation of Den Bosch on 14 december 1629 the Bossche confraternity continued to exist. In 1641 the Governor Den Bosch asked Johan Wolfert van Brederode and other prominent members among the new Protestant class to become a member of the Bossche Lieve Vrouwe confraternity. This was a very unusual step during this period because Catholics and Protestants would be a member of one association. After a fierce debate within the confraternity with 28 against 23 votes, it was decided to allow Protestants to the confraternity and new statutes were institutionalised. As a reason for the merge it was recorded in the statues that it was undesirable that Catholic and Protestant notables were hostile among eachother.
Organizational changes were made so that outside members were abolished and from now on the fraternity would consist of 18 Catholic and 18 Protestant members. A group of Orthodox preachers, including Reverend Voetius, was furious about the conversion of the confraternity which caused violent polemics. Finally the States of Holland put an end to the squabbling in 1646 and the statutes of the Brotherhood remained as they were drawn up in 1642, showcasing an oecumenical vision far ahead of it’s time. In 1818 the Prince of Orange, later King William II, was invited to the confraternity. Since then, many members of the Royal family have become a member.