On July 29, 1546, the anabaptists bought a built-up mill in Sobotište, together with a mansion from the countryman Klement Papp. It is clear from the chronicles of the anabaptists that the anabaptists came to Sobotiště from Moravia before 1546. The brothers had to leave the country by virtue of the law of 1548. Landlord of Branč estate František Ňári provided them with military protection up to the border with Moravia. Since the law of accepting anabaptists was valid also in Moravia, they lived together with the exiled brothers from the Bakič’s property for five weeks in the forests near Rohatec. Even before the forced departure of the brothers from Sobotište, F. Ňári bought two thirds of the mill from the anabaptists.
It seems that after the expulsion of the anabaptists in the autumn of 1548, the royal mandate was no longer applied, and after a few months the anabaptists gradually returned. In 1551 they are mentioned again in Sobotište. The effects of the Act of the Expulsion of the anabaptists from Hungary in 1557 were felt by the Sobotište anbaptists on September 1, 1557. Peter Diack (Deák) attacked their court, robbed them and plunged three brothers into prison. However, the brothers did not leave Sobotište. They did so only in 1581 because of disagreements with landlords – there were 12 co-owners of the estate – especially with Štefan Ňári. They used them without paying them for work. If they refused to work for free, they beat them. The dispute was settled only after ten years, when the brothers returned to Sobotište at the request of the landlords.
The riots and plunder associated with the anti-Habsburg uprisings and the Thirty Years’ War did not escape the fraternal courts. One evening in 1602, a group of soldiers robbed the Sobotište anabaptists of horses and other things worth 350 gold. On the night of 3. 5. 1605 Bočkajovci invaded the court. Fortunately, everyone managed to escape into the forest, except for two brothers who were killed by soldiers . Even in the forest they did not feel safe and therefore resorted to the castle Branč. The soldiers destroyed almost the entire court and so the brothers until Juraj in 1613 lived below the castle. Before moving back to Sobotište, the anabaptists concluded a new contract with the compossessorate of the Branč estate.
In connection with the Betlén uprising and riots in Moravia, brothers from the destroyed and looted Moravian courts sought refuge in Sobotište. But even the brothers in Sobotište were not safe. Polish soldiers camped at Strážnice took an unexpected attack on April 14, 1621 to Sobotište, where they plundered houses and killed several anabaptists.
After the defeat of the Bohemian and Moravian estates, the ruler Ferdinand II became the master of the situation and ordered all anabaptists to leave Moravia by the end of October 1622. Sobotište became the new center of the anabaptist until the violent recatholization in the early 1860s.