In the mid-13th century, it became a Freie Reichsstadt, an independent and republican self-ruled member of the Holy Roman Empire, controlling an area of approximately 220 square kilometres (85 sq mi) and 19 regional villages.

The theologian Thomas Müntzer, a leading person in the German Peasants' War, gave sermons here and was executed outside the city walls.

John A. Roebling, the constructor of the Brooklyn Bridge, and Friedrich August Stüler, an influential architect in mid-19th-century Prussia, were born in Mühlhausen.

Mühlhausen is within the Thuringian Basin, a flat and fertile area, on the Unstrut river on the eastern edge of the Hainich hills.

According to legend, in the 5th century Attila stayed at "Burg Mulhus" as a guest of his Thuringii allies before moving on to the Battle of the Catalaunian Plains.

[4]: 200  During the early 12th century, the "old town" was set up around the Untermarkt along the Hessenweg, an important trade route between the Kassel and the Erfurt regions.

[3]: 43 [4]: 200  In the early 13th century, the "new town" north of Schwemmnotte river followed with a regular grid around St. Mary's Church and Obermarkt with Steinweg as main streets.

The three cities pursued their own territorial policy (e.g. by buying castles) to protect their trade routes against robbery, which brought them constantly into conflict with local nobles.

Another aspect of the territorial policy was buying land and villages around the city, making use of any opportunity that presented itself, for example if local rulers (counts, monasteries etc.)

Mühlhausen bought 19 still existing and 43 later abandoned villages and an area of 220 km2 (85 sq mi) in this way, covering the north-western part of today's district Unstrut-Hainich-Kreis.

The monk and peasant leader Heinrich Pfeiffer from Reifenstein Abbey preached at St. Mary's in February 1523 for the first time, followed by Thomas Müntzer in August 1524.

Both had not only religious demands (they were members of the Anabaptist movement) but also political ones, aimed against the privileges of the magistracies and their oligarchic rule over the city.

[4]: 202  Among the works Bach composed while living in the town was an elaborate, festive cantata, Gott ist mein König, BWV 71, for the inauguration of the new council in 1708.

[3]: 43–44  The German mediatization led to the formal loss (that had de facto already occurred) of Mühlhausen's independence in 1803, as the city became part of Prussia.

The era of industrialisation and urbanisation reached Mühlhausen relatively late, around 1870, when the city was connected to the railway by a line from Gotha to Leinefelde.

In 1935, the Nazi armament campaign resulted in the building of a large military complex with several barracks with the deliberate side effect of boosting the city's weak economy.

Many exhibitions were set up (including some of the museums in Mühlhausen and the Bauernkriegspanorama near Bad Frankenhausen) and events celebrating the historical connection took place.

After reunification, many factories in Mühlhausen were closed, leading to another deep economic crisis with high unemployment rates during the 1990s and early 2000s.

Mühlhausen is situated in the flat landscape of the Thuringian Basin, a very fertile area covering the northern centre of Thuringia at an elevation of approximately 215 metres above sea level.

Germany's accurate geographical centre is located only 5 km (3 mi) south of the city in the neighbouring municipality of Niederdorla, where a monument can be found at this spot.

Mühlhausen abuts the following municipalities (all of them are part of the Unstrut-Hainich-Kreis): Anrode, Unstruttal and Menteroda in the north, Obermehler and Körner in the east, Vogtei in the south and Rodeberg in the west.

In the direction of Ammern (part of Unstruttal) there is no interruption in the build-up area, the Ruhrstraße forms an urban municipal border here.

[9] Mühlhausen had approximately 10,000 inhabitants during the late Middle Ages around 1500, which made it the second-largest number within today's Thuringia, after Erfurt, the current capital.

Mühlhausen fell back behind the new ducal residence cities like Weimar, Gotha or Altenburg in this period and lost its former importance.

Nevertheless, the population grew to 14,000 in 1850, 23,000 in 1880 and 35,000 in 1910, which was a significantly lower rate of growth than in other cities of comparable size during that period of rapid urbanisation in Germany.

It occurred after the reunification for a short time in the 1990s, but most of the suburban areas were situated within the administrative city borders, others were Unstruttal and Weinbergen.

[10] The most important regions of origin of Mühlhausen migrants are rural areas of Thuringia as well as foreign countries like Poland, Russia, Ukraine, Hungary, Serbia, Romania and Bulgaria.

Like other eastern German cities, foreigners account for only a small share of Mühlhausen's population: circa 1.6% are non-Germans by citizenship and 4.2% overall are classified as migrants (according to the 2011 EU census).

It was found near the city in large quantities and is both light and solid, so that the Gothic churches with their filigree masonries and other important buildings could be built relatively cheaply.

The region is a centre of the food industry in Germany, especially in the production of conserves like pickles, sauerkraut, apple sauce, cherries and other fruits and vegetables.