Next, Le Jeune settled in La Rochelle, a stronghold of the Huguenots, but sometime in the mid-1590s he must have returned to Paris, for his name appears in a list of musicians of the royal household of Henry IV both in 1596 and 1600. Few other details from late in his life are known, but he must have been composing prolifically, judging by the enormous quantity of music which remained in manuscript at his death, most of which was published in the first two decades of the 17th century. He died in Paris, and is buried in the Protestant cemetery of La Trinité.