In the Netherlands a movement for church reform developed into a struggle for Dutch independence. The Catholic emperor Charles V had inherited the seventeen provinces that compose present-day Belgium and the Netherlands (see "The Habsburgs"). In the Netherlands, as many other places, Lutheran ideas took root. Charles V had grown up in the Netherlands, however, and he was able to limit the impact of the new ideas. Charles V abdicated in 1556 and transferred power over the Netherlands to his son Philip II, who had grown up in Spain. Although Philip, like his father, opposed Protestantism, Protestant ideas spread in the Netherlands.

By the 1560s Protestants in the Netherlands were primarily Calvinists. When Spanish authorities attempted to suppress Calvinist worship and raised taxes, it sparked riots and a wave of iconoclasm. In response, Philip II sent twenty thousand Spanish troops, and from 1568 to 1578 civil war raged in the Netherlands between Catholics and Protestants and between the seventeen provinces and Spain. Eventually the ten southern provinces came under the control of the Spanish Habsburg forces. The seven northern provinces, led by Holland, formed the Union of Utrecht (the United Provinces), and in 1581 they declared their independence from Spain. The north was Protestant, and the south remained Catholic. Philip did not accept the independence of the north, and war continued. England was even drawn into the conflict, supplying money and troops to the United Provinces. Hostilities ended in 1609 when Spain agreed to a truce that recognized the independence of the United Provinces.