Allouez was born in Saint-Didier-en-Velay in the département of Haute-Loire in south-central France. In 1639, he graduated from the College of Le Puy, and became a Jesuit novice in Toulouse, France. In 1655, he was ordained a priest of the Roman Catholic Church. Allouez arrived in Quebec in 1658 and immediately began a study of the Wyandot and Anishinaabe languages to prepare himself for work as a missionary among the American Indian tribes along the St. Lawrence River for three years.
In 1660 he became the superior of the mission at Trois-Rivières, Quebec. His stay there lasted until 1663 when he was named vicar general of a part of the diocese of Quebec that is now the central region of the United States. This appointment was made by Bishop François de Laval, the first bishop of New France.
From 1667 through 1669 Allouez made a missionary tour of the western missions. He served as a missionary to the Potawatomi Indians in Wisconsin. The next year he was with the Mesquakie, establishing St. Mark's Mission, and founding the mission of St. James among the Miami and Mascouten Indians, finally returning to Green Bay later that year. He said the first Mass in Oconto, Wisconsin. In 1671, in Sault Ste. Marie, Michigan, he was a principal speaker at the ceremony that formally declared the Great Lakes and the Mississippi River valley as territory of the King of France. In 1671 he founded the St. Francis Xavier Mission at the last set of rapids on the Fox River before entering the Green Bay. The site was known as Rapides Des Pères (rapids of the fathers) which became modern day De Pere, Wisconsin. He continued Jacques Marquette's evangelizing of the Indians until his death in 1689, near what is today Niles, Michigan just north of South Bend, Indiana. He is buried in Niles.
A good portion of Father Allouez’s written work from the time has been preserved. It provides insight into the missions of the time and provides a record that is extensive and important of the Catholic Church in mid-America. It also contains the first documented accounts of the Illinois Indians. He died on his way back to France.
- The small village of Allouez, Wisconsin, near Green Bay, is named for him.
- Allouez Trail on Mackinac Island in Northern Michigan is named in his honor.
- Dictionary of Wisconsin History, s.v. Allouez, Claude Jean 1622 - 1689
- Who Was Who in America: Historical Volume, 1607-1896. Chicago: Marquis Who's Who, 1967.
- "Claude Allouez". Catholic Encyclopedia. New York: Robert Appleton Company. 1913.
- "Claude-Jean Allouez". Dictionary of Canadian Biography (online ed.). University of Toronto Press. 1979–2005.
- "Allouez, Claude Jean". The American Cyclopædia. 1879.