Contrary to some popular conceptions, Protestantism was not uprooted by the violence and cruelties of the Inquisition in the Southern provinces. On the contrary, these violences, under the Duke of Alba, only contributed to extend its influence. The Calvinist excesses of 1577-79 and the leniency of Farnese did more to counteract Calvinist propaganda than the wholesale massacres organized by the Council of Blood. It was against these persecutions, not against the Catholic religion, that the Southern provinces fought throughout the period of revolution, and the breaking off of all relations with the North automatically brought to an end the influence of Calvinism.
The rapid success obtained by Farnese's policy, and the fact that his successors had no need to have recourse to violent measures, shows that Protestantism was not deeply rooted in the South and that the people would have been only too pleased to agree to its exclusion if they had obtained in exchange peace and independence. But the war went on and the archduke was compelled to remain governor for Philip III.
This became apparent immediately when, in 1600, the States General claimed a voice in the administration of the country and in the control of expenditure. They met with a curt refusal and were obliged to agree to pay a regular subsidy in place of the old "special grants." The same year, Maurice of Nassau invaded Northern Flanders in the hope of provoking a rising, but the people did not answer to his call. The Spanish, however, were defeated at the battle of Nieuport, where the archduke was severely wounded. The next year began the siege of Ostend, which had remained faithful to the United Provinces and which was easily able to receive provisions by sea. After three years of struggle, the town was obliged to surrender, thanks to the skilful operations of Ambrose Spinola, who was placed at the head of the Spanish army. After further indecisive operations, a twelve years' truce was finally declared, on April 9, 1609, between the United Provinces and Spain. Philip III virtually recognized the independence of the Republic and even allowed the Dutch merchants to trade with the West Indies, a privilege which he had refused to his own subjects in Belgium. The Southern provinces were further sacrificed by the recognition of the blockade of the Scheldt, which remained closed to all ships wishing to enter Antwerp, to the greater benefit of Dutch ports.