Simultaneously with the trouble in France, Alva was engaged in "pacifying" the Netherlands. Here the Jesuits had miscalculated the strength of the Catholics, and, in encouraging the policy of violent repression, led to their own undoing. Only the favour of princes had secured some shelter for them in Belgium, and their houses now disappeared in the flames of the civil war. Their college at Douai had been interdicted by the university authorities in 1567, but relieved by papal authority. As the Spaniards proceeded, however, in the drastic and bloody policy which the Jesuits were known to favour, the crowds stormed their residences, and by 1570 they were almost driven from the country. They returned in the wake of Alva, but there was bitter hostility to them, and they were generally accused of rebuilding their house at Antwerp out of the loot of Flemish towns. Father Sacchini is moved to lament the perversity of men who could entertain such a suspicion, though, as their sardonic critic Steinmetz observes, "it would have been better to supply the place of this moral maxim by stating whence the funds were obtained for building or beautifying the house at Antwerp."
When we pass to Germany we naturally find that the Jesuits are apostles of toleration, charity, and calm intellectual discussion of differences of creed in the north, fanatical intolerantists in the south, and advocates of every conceivable compromise between the two extremes in the intervening or mixed States. Canisius still maintained his great work and his austere standard. Appointed Legate of the Pope in 1565 he traversed the whole of Germany on foot, and strengthened the loyalty of the Catholic rulers to the Council of Trent. In the following year we find him, at the Diet of Augsburg, helping to unite Protestants and Catholics against the Turk. Many new colleges were founded by him, including three in Poland, before the death of Borgia. On the other hand, grave reports had to be sent to Rome from the more Catholic and prosperous centres. The University of Dillingen, which the Jesuits controlled, was found in 1567 to be permeated with heresy, and a rigorous scrutiny ended in some of the Jesuits (including an English refugee, Edward Thorn) going over to the Protestants. In 1570 the Jesuit rector of Prague College became a Protestant and married. In Bavaria the cry was raised that they mutilated boys in their colleges. A most extraordinary trial resulted in their acquittal, but there was a deep and widespread prejudice against them. In the same year, 1565, they were fiercely assailed in Austria. Their college at Vienna was raided by an angry mob; and the nobles, who had been convoked by Maximilian, refused to give their aid in the campaign against the Turk unless the Emperor expelled the Jesuits.