There were 115 eventful years in Innsbruck's history between the last Count of Andechs and the first Tyrolean sovereign from the House of Habsburg. For around 100 years after the last Count of Andechs, the Counts of Tyrol controlled the destiny of the province and thus to a large extent the city of Innsbruck. Meinhard II of Tyrol (1239 - 1295) was able to expand his territory with skilful politics and a little luck. From his ancestral castle in Meran, he managed to unite the patchwork of what is now Tyrol into a more unified whole. His successor as Tyrolean ruler, Duke Henry of Carinthia (1265 - 1335), was one of the most important aristocrats in the Holy Roman Empire. However, he was not destined to have a male successor. Even before his death, however, Henry had ensured that his daughter Margarethe could succeed him.

Margarethe "Maultasch" of Tyrol-Görz (1318 - 1369) is one of the most famous female figures in Tyrolean history. She was married in her second marriage to Ludwig von Brandenburg, a Wittelsbach. As Dukes of Bavaria, the Wittelsbachs were the great adversaries of the Habsburgs within the Holy Roman Empire at the time. The problem was that Margarethe had not yet divorced her first husband, Johann-Heinrich von Luxemburg. This unloved Bohemian nobleman had been shooed out of the country by the Tyrolean population in 1341, but an official divorce was never finalised. The Pope imposed a curse on the province of Tyrol because of the "unholy" marriage of its sovereign princess. This interdict was one of the harshest punishments for people in the Middle Ages. It forbade the holding of masses and the giving of communion in the country's churches. It was probably at this time that Margarethe was nicknamed Maultasch was given. There are no contemporary portraits that would indicate a deformed mouth. The pictures we have of Margarethe Maultasch today date from the 16th century at the earliest.

Margaret's reign was characterised by several crises. The 14th century saw global warming in Europe, which resulted in a plague of locusts. This also led to crop failures and famine in Tyrol. But that was not all. From 1348 to 1350, Europe was ravaged by the plague. The disease probably travelled from Venice via Trento and the Adige Valley to Innsbruck. The Black death decimated the population and brought economic hardship and misery to the survivors. Not much information can be found in the archives, but the consequences of the plague were devastating, as they were throughout Europe. An Innsbruck woman who fell ill with the plague spoke in her will of the "common dying that is going on in the country".

People could not explain phenomena such as crop failures and plague. Many saw the devastation of the country as a punishment from God and held Margaret responsible, as the papal curse had been imposed on her account. The reasons probably lay elsewhere. Innsbruck was neither a paved city nor did it have the sewage system or drinking water supply that were to be established shortly afterwards. Animals and people shared the cramped space within the city walls under unsanitary conditions, which probably fuelled the Black Death more than the papal curse.

During this time, the Innsbruck Lower city pool in today's Badgasse. Baths were not only used for cleansing, medical care was also provided here by bathers according to the standards of the time. Bathers were travelling or local healers who treated the sick, stitched wounds or pulled teeth. The common doctrine up until modern times was the Four juices doctrine. According to this theory, there was a balance of blood, phlegm, black bile and yellow bile in the body. An imbalance of these juices leads to illness. The balance was disturbed by a blasphemous lifestyle, poor diet, excessive sexual activity or miasmas in the air. Water also had a reputation for penetrating through the skin and destroying the Juice ratio in the human body, which is why you should be treated after bathing. There were formally trained doctors at universities, but not many of them. The supernatural was considered real, even in medical care. The scientific approach of the universities of the time was not necessarily superior to that of the practice-orientated bathers.

During the 1350s, the Habsburg Rudolf IV (1339 - 1365) had campaigned for a reconciliation between the Pope and the princes of Tyrol, not entirely without self-interest of course. Margaret's son Meinhard III was married to Margaret of Austria, a Habsburg. Duke Ludwig died in 1361, and Meinhard also passed away in 1362. The treaty of succession drawn up in return for his intervention with the Pope regulated the succession in the County of Tyrol very favourably for the Habsburgs. With the consent of the Tyrolean nobility, Margarethe handed over the reins of government to Rudolf IV of Austria in 1363.

The Dukes of Bavaria from the House of Wittelsbach refused to recognise this inheritance treaty, which declared their claims to Tyrol null and void. As late as 1363, they moved towards Innsbruck in order to rectify the law by force of arms. The citizens of Innsbruck, who were obliged to do military service, were able to successfully defend the city, which was fortified by Andechsburg Castle and the city walls. It may be an irony of fate that it was the Wittelsbach Ludwig who had the city walls raised and reinforced.

Without Rudolf's unscrupulousness and his swindle, the history of Innsbruck would have been very different. With the acquisition of Tyrol, the Habsburg family was able to close an important geographical gap within its sphere of power. The incorporation of the city into the much larger territory of the Habsburgs gave Innsbruck additional importance, while the actual capital of Merano was further marginalised. In addition to the north-south transport of goods, the city on the Inn had now also become a west-east transport hub between the eastern Austrian lands and the old Habsburg possessions in the west. At the same time, the survivors of the great plague wave of 1348 led to an economic boom throughout Europe. Labour had become scarce due to the shrinking population, but greater resources were available per capita. For the people of Innsbruck, who had survived the turbulent first half of the 14th century, better times were about to begin.