In the course of 16th century the situation calmed down and devastating war events avoided this area. The Jesuits came to Haná, they recatholized the population and disseminated education.
Dormitory and Jesuitical grammar school, promoted already in 1573 by the pope Řehoř VIII. and by emperor's decree of Maxmillian II. to a university, was built in Olomouc.
However, the period of peace was disrupted by the events of Thirty Year's War. In 1619 professional army appeared in the Olomouc region and plundered several villages there. However, the region suffered from the most serious strike in the final stage of this European conflict. In 1643 the Swedes invaded Moravia and conquered Přerov, Prostějov and after a massive siege also Olomouc. They stayed here for the whole 8 years and were driven off as late as 1650, two years after peace had been concluded. Before the town was occupied, all municipal authorities were relocated to Brno and stayed hereafter and Olomouc lost its position of the capital town of Moravia. The consequences of the Thirty Year's War were horrible - out of original 32 000 inhabitants of Olomouc only 2500 of them remained alive, neighbouring towns were plundered and every fifth village ceased to exist. According to estimations referring to the entire Moravian region, the whole one third of inhabitants died from hunger, slaughter and diseases to which the population, bothered by war suffering, was more vulnerable.