While a novice in the Jesuit religious order at Bordeaux, France, Labadie claimed a vision to reform the church. In 1639, however, seriously ill and increasingly dissatisfied with the Jesuits, he obtained their permission to leave the order. In 1644 Labadie founded several small societies dedicated to frequent communion and holy life. Called pietistic for their stress on the practice of godliness, these communities influenced similar ones begun later by the founder of the German Pietist movement, P.J. Spener (1635–1705). Growing opposition from both civil authorities and the Jesuits caused Labadie to change residence several times. After reading John Calvin's Institutes of the Christian Religion (1536), he declared formal allegiance to the Reformed Church at Montauban in October 1650 and became professor of theology there the same year. Expelled for unorthodoxy in 1657, he sought refuge in Orange and then in 1659 in Geneva, where Spener heard him preach. In 1666, after being suspended from his ministry in the French church at Middleburg, Labadie fled to Amsterdam, where he founded a separatist group of Pietists. Excommunicated from the Reformed Church in 1670, he went with his group to Herford and then two years later to Altona, the Mennonite sanctuary.

By that time the basic Labadist principles centred upon an existence in which goods and meals were held in common. Labadie taught that the church consisted only of those regenerated by the Holy Spirit and asserted that the sacraments could be administered to them alone. He became increasingly separatist in his views during his later years, and his community never grew beyond a few hundred members. Although Labadist colonies were established by emigrants to the Western Hemisphere, they did not survive past 1730. The remaining community in Europe, at Wiewert, in West Friesland (now in The Netherlands), was dissolved in 1732. Among Labadie's more than 70 writings is La Réforme de l'église par le pastorat (1667; “The Reform of the Church Through the Clergy”).