It is conjectured that Marguerite gave Anne the original manuscript of Miroir de l'âme pécheresse at some point. It is certain that in 1545, sometime after Anne Boleyn's execution by her husband Henry VIII, that Anne's daughter, who would become Elizabeth I (1533–1603), translated this very same poem by Marguerite into English when she was twelve years old and presented it, written in her own hand, to her then-stepmother, the English Queen Katherine Parr. This literary connection among Marguerite, Anne, Katherine Parr, and the future Queen Elizabeth I suggests a direct mentoring link between the legacy of reformist religious convictions and Marguerite.

As a generous patron of the arts, Marguerite befriended and protected many artists and writers, among them François Rabelais (1483–1553), Clément Marot (1496–1544), and Pierre de Ronsard (1524–1585). Also, Marguerite was mediator between Roman Catholics and Protestants (including John Calvin). Although Marguerite espoused reform within the Catholic Church, she was not a Calvinist. She did, however, do her best to protect the reformers and dissuaded Francis I from intolerant measures as long as she could. After her death, six "Catholic Wars" occurred, including the terrible "St. Bartholomew's Day Massacre" of 1572.

Eminent American historian Will Durant wrote: "In Marguerite the Renaissance and the Reformation were for a moment one. Her influence radiated throughout France. Every free spirit looked upon her as protectoress and ideal .... Marguerite was the embodiment of charity. She would walk unescorted in the streets of Navarre, allowing any one to approach her and would listen at first hand to the sorrows of the people. She called herself 'The Prime Minister of the Poor'. Henri, her husband, King of Navarre, believed in what she was doing, even to the extent of setting up a public works system that became a model for France. Together he and Marguerite financed the education of needy students."

Jules Michelet (1798–1874), the most celebrated historian of his time, wrote of her: "Let us always remember this tender Queen of Navarre, in whose arms our people, fleeing from prison or the pyre, found safety, honor, and friendship. Our gratitude to you, Mother of our [French] Renaissance! Your hearth was that of our saints, your heart the nest of our freedom."

Pierre Bayle (1647–1706), French philosopher and critic, whose Dictionnaire historique et critique (Historical and Critical Dictionary, 1697) greatly influenced the French Encyclopedists and the rationalist philosophers of the eighteenth century, such as Voltaire and Diderot, esteemed her highly, writing: "... for a queen to grant her protection to people persecuted for opinions which she believes to be false; to open a sanctuary to them; to preserve them from the flames prepared for them; to furnish them with a subsistence; liberally to relieve the troubles and inconveniences of their exile, is an heroic magnanimity which has hardly any precedent ..."

Leonardo da Vinci (1452–1519) died while guest of Marguerite and her brother, Francis I. They had been raised at Château d'Amboise, which belonged to their mother, Louise of Savoy. The king maintained his residence there and Marguerite maintained a residence nearby. During the first few years of the reign of Franics the château in which he lived reached the pinnacle of its glory. da Vinci had been the architect of a large château for them, among many other projects, and they provided quarters for him when he left Italy and joined her court. As a guest of the king, who provided him with a comfortable stipend, Leonardo da Vinci came to Château Amboise in December 1515 and lived and worked in the nearby Clos Lucé, connected to the château by an underground passage. Tourists are told that he is buried in the Chapel of Saint-Hubert, adjoining the Château, which had been built in 1491–96.

In 1550, one year after Marguerite's death, a tributary poem, Annae, Margaritae, Ianae, sororum virginum heroidum Anglarum, in mortem Diuae Margaritae Valesiae, Nauarrorum Reginae, Hecatodistichon, was published in England. It was written by the nieces of Jane Seymour (1505–1537), third wife of King Henry VIII.

Marguerite de Navarre's ancestors in three generations are,

Marguerite was married twice, first to Charles IV of Alençon, but the marriage was childless.