In the wake of the German Peasants' War Allschwil, together with Reinach, Therwil, Oberwil and Ettingen, joined Basel in 1525 with a Burgrecht agreement. This agreement was dissolved in 1585 in the Baden Agreement. In 1529 the village embraced the Protestant Reformation and converted to the new faith. Nearly a hundred years later, in 1627, the Bishop of Basel succeeded in spreading the Counter-Reformation to Allschwil. After 1567 there was a Jewish settlement in Allschwil. In 1692 there were 24 Jewish families living in the "Judengässlein" (from ) and they made up about 15% of the population. They had their own cemetery in Zwingen and a funeral right in Hegenheim. Children of Jews and Christians attended the 17th-century school together. Accusations of horse theft and Jewish plans to build a synagogue in Allschwil led to an expulsion decree in 1694 from the Bishop. Many of the Jews fled to Hegenheim.