Colmar is one of the oldest communities in Alsace and a synagogue is mentioned as early as in the 13th century, destroyed by fire in 1279. During the massacre of the Jews, burned alive in 1349, the city confiscated the synagogue. The Jewish community and its synagogue began again around 1380 but vanished in 1512, when Colmar expelled the Jews. Again, the synagogue was confiscated by the city.
During the revolution, some Jews were able to return to Colmar. In 1823, the consistory based in Wintzenheim, the largest community in the Upper Rhine, was transferred to Colmar.
After praying in various oratories, the community built a monumental synagogue, in a neo-Romanesque style, which was inaugurated on September 15th 1843. It was renovated in 1885 and 1913, with the addition of an extra gallery for women, and the replacement of the central wooden platform by a sandstone platform. During World War II, the Germans used the synagogue as an auction house for furniture stolen from expelled Jews, and then turned it into an arsenal. The ransacked building was restored after the Liberation and inaugurated in 1961. The synagogue has been registered as a historical monument since July 1984.