It was in 1526 that Papacy made the call for disputation at Baden on 16th of May with a view to confronting the growing power of the Reformation in Switzerland. Zurich City Council, understanding the potential risk that Zwingli might get arrested or even murdered if he went for the debate, encouraged him to turn down the call to go to the debate. They selected instead two of Zwingli's fellow workers, Oecolampadius and Haller, to carry the Reformation standard in the disputation. The Papacy selected instead to send the very renowned Dr. Eck, the individual who had argued Martin Luther in Leipzig in 1519, to defend Catholic orthodoxy.

While Zwingli was not present in body at the disputation, he was permitted to participate in spirit. He smuggled letters to his reforming allies backstage, using guileful strategies to cover up his actions. One such means was sending communications under baskets of poultry placed upon the heads of farmlands, a quiet but astute method of transmission that allowed Zwingli to offer advice and encouragement to the reformers.

The debate raged on for eighteen days, each side presenting its argument. The Papacy finally emerged victorious, but the actual legacy of the event was its impact on spreading the Reformation throughout Switzerland. While the Papacy had its official victory, the debate itself solidified the Reformation's presence and voice, as the ideas of reform began to solidify more strongly within Swiss society. The Baden disputation was a turning point, generating momentum for the Reformation across the region.