The first years of Emperor Ferdinand I's reign (1503 - 1564) as sovereign of Tyrol were characterised by theological and social unrest. Theological and social tensions increased during this crisis-ridden period. The new law, which had been introduced by Maximilian's administration, stood in opposition to the old customary law. Hunting in the forest and searching for firewood had thus become illegal for the majority of the population. Siegmund's lavish court management and Maximilian's wars, including the pledging of a large part of the state's assets, had put Tyrol's financial situation in dire straits. At this time, two men emerged in Tyrol, Jakob Hutter (1500 - 1536) and Michael Gaismair (1490 - 1532), who threatened the existing order and paid for it with their lives.

Jakob Hutter was the figurehead of the Anabaptists, who were mainly active in the Inn Valley and the Puster Valley in South Tyrol. The first signs of the Little Ice Age caused an increase in crop failures. Many people saw this as a punishment from God for people's sinful lives. Sects such as the Anabaptists preached the pure doctrine of religion in order to free themselves from this guilt and restore order. The Roman Church and the pious Prince Ferdinand were particularly displeased by their attitude towards worldly possessions and baptism. People should freely express their will to join Christianity as adult and responsible citizens and not be baptised as children. The Anabaptists posed a threat to public order for the strictly religious Prince Ferdinand, who was loyal to the Pope, and were welcome scapegoats for the majority of Tyroleans. As early as 1524, three Anabaptists were burned at the stake for heresy in front of the Golden Roof in Innsbruck. Five years later, thousands of Anabaptists were expelled from the country and emigrated to Moravia, today's Czech Republic.

One of them was Jakob Hutter. Having grown up in South Tyrol, his apprenticeship and journeyman years as a hatter took him to Prague and Carinthia, where he probably first came into contact with the Anabaptists and their teachings. When the religious community was also expelled from Moravia in 1535, Jakob Hutter returned to Tyrol. He was captured, taken to Innsbruck and imprisoned in the Kräuterturm gefoltert. Er fand als Anführer der Häretiker für sein Wirken 1536 vor dem Goldenen Dachl his end at the stake.

The community of Hutterischen Brüder kam nach ihrer endgültigen Vertreibung aus den deutschen Ländern und langen Irrfahrten und Fluchten quer durch Europa im 19. Jahrhundert in Nordamerika an. Noch heute gibt es einige hundert Hutterer Kolonien in Kanada und den USA, die noch immer nach dem Gebot der Jerusalemer Gütergemeinschaft in einer Art kommunistischem Urchristentum leben. Wie die Mennoniten und die Amisch leben die Hutterer meist isoliert von der Außenwelt und haben sich eine eigene Form der an das Deutsche angelehnten Sprache erhalten. In Innsbruck erinnern eine kleine Tafel am Goldenen Dachl sowie eine Straße im Westen der Stadt an Jakob Hutter. 2008 hatten die Bischöfe von Brixen und Innsbruck gemeinsam mit den Landeshauptleuten Nord- und Südtirols in einem Brief an den Ältestenrat der Hutterischen Brüder das knapp 500 Jahre vergangene Unrecht an der Täufergemeinschaft eingestanden. 2015 wurde im Saggen eein paar Schritte südwestlich des Panoramagebäudes der Huttererpark eröffnet, in dem das Denkmal „Übrige Brocken“ an das Schicksal und Leid der Verfolgten erinnert.

Der größte Aufruhr im Zuge der Reformation in Tirol war der Bauernaufstand ab 1525, der eng mit dem Namen Michael Gaismairs verbunden ist. Anders als Hutter, der vor allem eine spirituelle Erneuerung forderte, wollte Gaismair auch soziale Veränderungen vorantreiben. Der Tiroler Aufstand war ein Teil dessen, was als Deutscher Bauernkrieg große Teile des Heiligen Römischen Reiches was shaken. It was partly reformist, theological fervour and partly dissatisfaction with the social situation and distribution of goods that drove the rebels. Unlike Martin Luther, Gaismair was not a theologian. He was the son of a mining entrepreneur, one could say educated middle class. While working in the service of the Bishop of Brixen, he saw how the sovereign administration and jurisdiction treated the subjects. In May 1525, he took part in the uprising against the clergy in Brixen. A mob invaded the Neustift monastery and the bishop's property. The enraged subjects plundered the monastery and destroyed the Urbare, the records of the peasants' property, debts and obligations to the lord of the manor. The bishop was also a secular prince and was regarded as a particularly strict sovereign.

The movement quickly gained momentum and spread rapidly. Uprisings took place throughout the country. In Innsbruck, Wilten Abbey, the seat of the landlord of many subjects, was besieged. Gaismair was chosen by the rebels as captain to conduct negotiations with the Tyrolean prince, Ferdinand I, at the provincial parliament in Innsbruck. He drew up a utopian type of provincial constitution. His intention was not to shake Prince Ferdinand himself, but to ask him to Namen Gottes to organise and administer the country more fairly. The clergy were to concern themselves with the salvation of their subjects instead of politics. Land and goods such as mining yields were to be distributed in a socially just manner and interest was to be cancelled. The restrictions on hunting and fishing imposed on the Tyroleans by Ferdinand's predecessor Maximilian I (83) were to be lifted. These concerns were emphasised in the 62 Merano articles collected later on 96 Innsbruck articles have been expanded.

When Gaismair and his delegation negotiated with Ferdinand and his officials in Innsbruck in June 1525, he was arrested and imprisoned in the Kräuterturm imprisoned. After almost two months in prison, he was able to escape and continue his fight from Sterzing. After several defeats, he went to neighbouring Switzerland, which was in revolt against the Habsburgs, where he met the reformer and revolutionary Huldyrich Zwingli. It was here that he wrote down his social-revolutionary national order, which envisaged a Christian state of peasants, craftsmen and miners in which goods were to be communitised. One of the articles read:

„As far as the tithe is concerned, everyone should give it according to the commandment of God, and it should be used as follows: Let every parish have a priest according to the teaching of the Apostle Paul, whom the word of God proclaims to the people... what is left over is to be given to the poor."

He was also the army commander of the resistance group against the Habsburgs. The reputation of his military successes reached the Republic of Venice, which had been in constant conflict with the Habsburgs since the war with Siegmund the Rich in Coin in 1477. Gaismair was recognised as Condottiereas an army commander. However, he soon fell out of favour here too. Not only did Venice make peace with the Habsburgs, but his anti-Catholic stance and non-conformist lifestyle also aroused envy and envy. In 1532, he was murdered at his country estate near Venice with more than 40 stab wounds. It is not clear which of the many powers he had set against him was behind this.

No less interesting than his life is his post-mortem career. Gaismair never made it to the general fame of Andreas Hofer in Tyrol. To this day, he is hardly ever talked about in schools. Unlike Hofer, who rose up as a good Catholic against a foreign power, Gaismair was an insurgent, an unpleasant and lateral thinker. A play about the peasant leader by Franz Kranewitter was published in 1899. In the 20th century, Gaismair was interpreted as a fighter against the monarchy and clergy, by the National Socialists as a German hero and liberator of the peasants or by the left as an early communist. The generation of 1968 celebrated the actually pious and God-fearing revolutionary for his ideas on the communisation of property. The Tyrolean journalist and historian Claus Gatterer wrote about the constant reinterpretation of the figure of Gaismair:

 „How much truth is a people allowed to know about its past, about the growth and development of its present? .... According to the respective ideology, long-deserved heroes and saints are toppled from their pedestals and replaced by others who have been disregarded until then; or an established saint is given a new biography without further ado, which fits in with current requirements in terms of the motivation for action.“

Unlike Andreas Hofer, there are hardly any memorials in Innsbruck to Michael Gaismair and the peasant uprising of 1525. A street and a secondary school in Wilten commemorate him.