Moutier is first mentioned in 1154 as datum Monasterii. In 1181 it was mentioned as apud Monasterium. The German name for the town is Munster (BE), but it is not frequently used.
The area was lightly settled even before the founding of Moutier-Grandval Abbey around 640. Much of the early history of the village is closely connected with the Abbey. Between 1049 and 1150 the Abbey was granted a stift or land donation to support the college of canons. The stift allowed the Abbey to grow into a major landholder and a regional power. The village church of Saint-Pierre, which eventually became a parish church, was probably built during the Early Middle Ages. In the 12th century another monastery was founded in Moutier, but it was destroyed in a fire in 1269. In addition to the Church of Saint-Pierre, the collegiate church of Saint-Germain and Saint-Randoald was built in Moutier during the 12th century. Everything changed in Moutier after the Protestant Reformation was accepted by Bern in 1531. The Abbey closed and the college of canons relocated to Delemont. The church of Saint-Germain and Saint-Randoald was closed while the church of Saint-Pierre converted to the new faith and was expanded. A fire destroyed the church of Saint-Germain and Saint-Randoald in 1571 though in 1860-63 a Reformed church was built on the site. The church of Saint-Pierre was demolished in 1873. Today Moutier has both German and French speaking churches.
After the college of canons of the Abbey moved to Delemont, the Abbeys properties in and around Moutier fell under the Prince-Bishop of Basel. The Bishop appointed a provost to manage the Abbeys estates and around the end of the 16th century, built the Provosts Castle. The provost remained in Moutier until 1797. After the 1797 French victory and the Treaty of Campo Formio, Moutier became part of the French Departement of Mont-Terrible. Three years later, in 1800 it became part of the Departement of Haut-Rhin. After Napoleons defeat and the Congress of Vienna, Moutier was assigned to the Canton of Bern in 1815. Two years later, in 1817, the Canton of Bern acquired the castle and used it as the seat of the district governor.
During the 19th century and early 20th century, Moutier developed into a transportation hub. In 1876 a railway opened between Basel and Moutier. This first railroad was followed by a route to Biel through the Tavannes valley in 1877 and then to Solothurn in 1908. In 1915 the 8.6 kilometers (5.3 mi) long Grenchenberg tunnel connected Moutier and Grenchen. The extensive road and railroad network encouraged Moutier to industrialize, with three industries, glass-making, watchmaking and automatic lathes, gaining international recognition for Moutier.
In 1842 Celestin Chatelain founded the Verrerie de Moutier glass factory. They became the most important window glass manufacturer in Switzerland and by the 1970s produced 250 tons of glass per month to meet Swiss domestic demand. The conversion from glass rolling to float glass spelled the end of the old Moutier glass factory, it closed in 1978. However, a subsidiary, Verres Industriels SA, had been created in 1955 and they began producing glass with the new process. Today Verres Industriels employs about 200 people.
Watchmaking first spread throughout the Jura region as a cottage industry during the 19th century. In the late 19th century the Grande Fabrique was built in Moutier and by 1880 employed about 500 workers. A number of watchmakers opened factories in the town, of which Leon Levy & Freres and Louis Schwab were some of the largest. However, many of Moutiers independent watchmakers went bankrupt and were forced to close during the Great Depression. Those that survived this period were generally absorbed by ETA SA in the 1950s.
In 1883 Nicolas Junker founded the Junker & Cie company to manufacture automatic lathes with a moveable headstock. After a bankruptcy and several name changes the company became Usines Tornos, Fabrique de machines Moutier SA in 1918. In 1968 Tornos bought the Petermann SA company to become Tornos Petermann. They then merged in 1974 with Bechler SA to become Moutier Machines Holding, which became Tornos-Bechler SA in 1981. It was renamed to Tornos SA in 2001. Over its nearly a century in operation, Usines Tornos built workers housing, provided jobs and vocational training and helped drive Moutiers growth. At its peak in 1974, the company employed about 3,000 people. Between 1980 and 2000, the company acquired and sold off several companies and reduced its headcount to about 1300 in 2001. In 2010 the company employed 855 people, including 655 in Moutier.
In 1950, Moutier became a city and a number of construction projects followed. A swimming pool opened in that same year. In 1955 a second primary school opened along with a new building for the secondary school. A new train station opened in 1961. In 1962 the old secondary school was converted into a town hall. A primary school in Chantemerle opened in 1973 and a new district hospital was built in 1976. There are two museums in town, the villa Bechler with the Jurassic Museum of Arts and the villa Junker with the Museum of Automatic Lathes.
Politically, the issue of Jurassic separatism is a major issue in Moutier. In 1974 a plebiscite voted to remain part of Bern by a margin of only 70 votes. This led to acts of vandalism on 16 March 1974 and on 7 September 1975 an armed standoff at the Hotel de la Gare which was broken up by an elite team of Bernese police on the following day. Two other plebiscites also came down on the side of remaining in the Canton of Bern, including one in 1998 which passed with a thin majority of 41 votes. Another plebiscite is planned for late 2013.
Moutier has an area of 19.58 km2 (7.56 sq mi). As of 2012, a total of 5.84 km2 (2.25 sq mi) or 29.8% is used for agricultural purposes, while 10.76 km2 (4.15 sq mi) or 55.0% is forested. Of the rest of the land, 2.73 km2 (1.05 sq mi) or 13.9% is settled (buildings or roads), 0.18 km2 (0.069 sq mi) or 0.9% is either rivers or lakes and 0.11 km2 (27 acres) or 0.6% is unproductive land.
During the same year, industrial buildings made up 1.3% of the total area while housing and buildings made up 6.9% and transportation infrastructure made up 3.5%. Power and water infrastructure as well as other special developed areas made up 1.5% of the area Out of the forested land, 52.4% of the total land area is heavily forested and 2.6% is covered with orchards or small clusters of trees. Of the agricultural land, 3.7% is used for growing crops and 14.1% is pastures and 11.6% is used for alpine pastures. All the water in the municipality is flowing water.
The area around Moutier is called the Prevote. It is a valley crossed by a river called the Birs. It covers the area from Court Gorge to Moutier Gorge and includes some scattered farm houses on the Montagne de Moutier (Moutier Mountain).
On 31 December 2009 the District de Moutier, of which it was the capital, was dissolved. On the following day, 1 January 2010, it joined the newly created Arrondissement administratif Jura bernois.
The area has a lot of factories that produce high-precision machine tools, particularly CNC & CAD/CAM machining centers, including Tornos Bechler SA & Schaublin Machines SA.