In 1412, papal emissaries arrived in the city with a papal bull authorizing them to sell indulgences. On 7 June, Hus spoke out against this simony in a public disputation, making use of the ideas of Wyclif. Some of the University masters (such as Štěpán Páleč and Stanislav of Znojmo) openly condemned several of Wyclif's main theses. Hus championed Wyclif's cause, publishing his tracts on this subject under the title “Defensio quorandum articulorum Joannis Viklef” (“A defence of some off Wyclif's articles”). The dispute now took a turn for the worse.

In July, Hus presided over the funeral in Bethlehem Chapel of three craftsmen, Jan, Martin, and Stašek, who had been arrested during riots caused by the indulgences and then executed under sinister circumstances. Prague was placed under interdict (no church offices, including baptisms, funerals, and masses, were allowed to be held in the city while Hus remained there), and the king was also threatened with a papal anathema. Hus therefore left Prague in November. Before leaving, he took a step which truly made him a reformer “in the grand style” he appealed to a higher authority, which is not recognized in canon law, but which is the decisive one for every Christian: to his personal saviour and judge Jesus Christ (18 October 1412). After his departure he stayed mainly in the countryside, especially in Kozí Hrádek near Tábor, but he often travelled to Prague, for the situation there had quietened down somewhat.

During his stay in the countryside Hus preached in the Czech language to the ordinary people and also produced a number of writings. In 1412, he wrote “The Creed, the Ten Commandments and the Paternoster,” and “The three-source string,” the following year “Concerning simony,” “A large mirror for a sinner,” “Daughter,” and “Concerning the six heresies,: and in 1414 “The essence of Christian teaching.” In the winter of 1412-1413 he produced the important Latin tract “De ecclesia” (“Concerning the church,”) which summarizes his teachings. Although in form this work owes much to Wyclif, whom it often quotes or paraphrases, it is an original work of some consequence. Of course it is not always in agreement with church traditions, but its basic intention is clear: it wants a church without stain or blemish. In 1413 Hus also wrote several responses in Latin to the accusations of his opponents.

In the autumn of 1414, a Council was convened in Constance, so that order might finally be restored in the Church. Hus decided to travel to the Council. From the summer of 1414 onwards he lived near Rakovník in the mansion of Krakovec, preached in the area, and prepared for the journey to Constance. It was at this time that he wrote the famous “Sermo de pace” (“Discourse on peace,”) with which he wanted to address the Council.

On 14 October 1414, Hus set out from Prague, in the company of leading Czech nobles. On 3 November, he arrived in Constance, but on 28 November he was arrested and kept in prison in various places in and around the town. On several occasions he was called before the Council and put under pressure to recant his views. While in prison he wrote several shorter tracts and a number of moving letters. He refused to recant, asking for an explanation of where he was in error. He was condemned as an intractable heretic and burned at the stake on 6 July 1415. Afterwards, his ashes were scattered in the Rhine.

Hus’s death provoked riots in the Czech lands and led to conflicts which lasted for centuries. However, it did demonstrate the genuine commitment - as we would say today ~ of Master Jan Hus to the truth of Christ and to a genuine, pure and moral life of the individual and of society, for which he was prepared to sacrifice his own life.