Although he anticipated some ideas that were important to the Protestant Reformation, Lefèvre remained a Roman Catholic throughout his life, and sought to reform the church without separating from it. Several of his books were condemned as heretical, and he spent some time in exile. He was, however, a favorite of the king of France, Francis I, and enjoyed his protection.
He visited Italy before 1486, for he heard the lectures of Argyropulus, who died in that year; he formed a friendship with Paulus Aemilius of Verona. In 1492 he again travelled in Italy, studying in Florence, Rome and Venice, making himself familiar with the writings of Aristotle, though greatly influenced by the Platonic philosophy. Returning to the University of Paris, he became professor in the college of Cardinal Lemoine. Among his famous pupils were F. W. Vatable and Guillaume Farel; his connexion with the latter drew him closer to the Calvinistic side of the movement of reform. Farel joined Lefèvre at Meaux to help in the training of preachers, before Farel left for Switzerland where he was one of the founders of the Reformed churches.
In 1507 he took up his residence in the Benedictine Abbey of St Germain des Prés, near Paris; this was due to his connexion with the family of Briconnet (one of whom was the superior), especially with Guillaume Briçonnet, cardinal bishop of Saint-Malo, father of Guillaume Briçonnet, the later bishop of Meaux. He now began to give himself to Biblical studies, the first-fruit of which was his Quintuplex Psalterium: Gallicum, Romanum, Hebraicum, Vetus, Concilialum (1509); the Conciliatum was his own version. This was followed by S. Pauli Epistolae xiv. ex vulgata edition, adjecta intelligentia ex Graeco cum commentariis (1512), a work of great independence and judgment.
His De Maria Magdalena et triduo Christi disceptatio (1517), which argued that Mary the sister of Lazarus, Mary Magdalene and the penitent woman who anointed Christ's feet were different people, provoked violent controversy and was condemned by the Sorbonne (1521) and Saint John Fisher. He had left Paris during the whole of 1520, and, removing to Meaux, was appointed (May 1, 1523) vicar-general to Bishop Briconnet, and published his French version of the New Testament (1523). This (contemporary with Luther's German version) has been the basis of all subsequent translations into French. From this, in the same year, he extracted the versions of the Gospels and Epistles "a l'usage du diocese de Meaux." The prefaces and notes to both these expressed the view that Holy Scripture is the only rule of doctrine, and that justification is by faith alone.
He incurred much hostility, but was protected by Francis I and his intellectual sister Marguerite d'Angouleme. Francis being in captivity after the battle of Pavia (February 25, 1525), Lefèvre was condemned and his works suppressed by commission of the parlement; these measures were quashed on the return of Francis some months later. He issued Le Psautier de David (1525), and was appointed royal librarian at Blois (1526); his version of the Pentateuch appeared two years later. His complete version of the Bible (1530), on the basis of Jerome's Vulgate, took the same place as his version of the New Testament. The publication and its revised edition based on the Hebrew and the Greek texts were printed by Merten de Keyser in Antwerp in 1534. Marguerite (now queen of Navarre) led him to take refuge (1531) at Nerac from persecution. He is said to have been visited (1533) by John Calvin on his flight from France. He died in 1536 or 1537.
Also the publication, with critical apparatus, of Boetius, De Arithmetica.,
He was a prolific translator of the Bible. He completed a translation of the Old Testament in 1528, and was famous for his French translation of Psalms and the Pauline epistles, which he finished early in his career. His completed translation of the entire Christian Bible, published in 1530, was the first in the French language.