During the 16th Century, when Philip II was King of Spain, he was also governor of the Netherlands. Unfortunately, he was not very tolerant of any religion other than Catholicism. So this made it hard for him to deal peacefully with the Protestants. While Philip was never actually in the Netherlands, his sister Margaret, Duchess of Parma was living in the Netherlands as regent. And what she saw was that the Protestants were very tolerant towards all and that nobody was forced to do anything against their will. However, because Philip didn’t believe in religious toleration, he tried to stem the protestant growth in the Netherlands by instating the Inquisition. There were many different times in Europe when the Inquisition was used, but this was a time when the Protestants were not allowed any religious freedom and were persecuted. It was religious prejudice.
A bit fearfully, Margaret wrote to Philip pleading with him to stop the Inquisition because in the Netherlands was very happy. So Philip did the right thing and gave the Protestants some space. But what worried him next was that the Protestants were now having large gatherings, and they were all showing up armed. This made Philip start to think that maybe he had been too nice to them. Had he? Philip began receiving reports about more large gatherings and how Catholic churches and houses were being vandalized by Protestants now as well. Now that was it for Philip, he immediately organized a 10,000 strong army, led by the Duke of Alba to get the Protestants under control. He didn’t reinstate the Inquisition, but it was still just as bad. The Duke of Alba also issued a 10% tax increase, which added to the mix of the Protestants’ anger and frustration. No matter what the King did, he could no longer contain the revolting Protestants.
The revolt finally ended in 1648, long after all the people who had started it in 1568 were dead, and when the Treaty of Münster was signed and gave the Protestants religious freedom. The Netherlands as a whole was also given its own freedom.
You can read more about the Dutch Revolt and the Treaty of Münster here: