A ducal commission, appointed to find a means for ending the interminable strife between the rival academic parties, entrusted Eck with the preparation of fresh commentaries on Aristotle and Petrus Hispanus.
At Baden-in-Aargau in May and June 1526 a public disputation on the doctrine of transubstantiation was held, in which Eck and Thomas Murner were pitted against Johann Oecolampadius.
Meanwhile at Rome the pope had entrusted Eck and Prierias with the preparation of a bull (Exurge Domine) against Luther - a bull which followed the line of Eck's charges at Leipzig.
This duke, however, at whose instigation the famous discussion between Luther and Johann von Eck took place in the Pleissenburg of Leipzig, inflicted some injury upon the town's trade and also upon its university by the harsh treatment which he meted out to the adherents of the new doctrines; but under the rule of his successor, Henry, Leipzig accepted the teaching of the reformers.
Bishops, universities and humanists were at one in denunciation of the outrage; and as for the attitude of the people, Eck was glad to escape from Saxony with a whole skin.
It was not, however, until after the Leipzig disputation with Eck that Luther won his allegiance.
Though Eck claimed the victory in argument, the only result was to strengthen the Swiss in their memorial view of the Lord's Supper, and so to diverge them further from Luther.
Melanchthon replied in a brief and moderately worded treatise, setting forth Luther's first principle of the supreme authority of Scripture in opposition to the patristic writings on which Eck relied.
Kohler, Luthers 95 Theses sammt seinen Resolutionen, den Gegenschriften von Wimpina-Tetzel, Eck and Prierias, and den Antworten Luthers darauf (Leipzig, 1903); Emil Reich, Select Documents illustrating Medieval and Modern History (London, 1905); The Leipzig Disputation: Seidemann, Die Leipziger Disputation im Jahre 1519 (Dresden, 1843); Luther before the Diet of Worms: Deutsche Reichstagsakten unter Kaiser Karl V.
At the Augsburg diet in 1530 Eck was charged by Charles V.