The character known as the Comte de Saint-Germain in Le Chevalier D'Eon is a figure shrouded in profound mystery, whose actions drive much of the story's occult conflict. The narrative provides no concrete information about his background or origin before his appearance in Paris. He is instead presented as an enigmatic and seemingly immortal force whose true nature and age are never fully explained, though he is frequently associated with the practice of alchemy and the supernatural arts.

Saint-Germain's personality is marked by an unsettling, almost playful detachment from the events around him. He carries himself with a calm, unshakable demeanor and a sense of superiority that stems from his immense power and long experience. His actions are not driven by loyalty to any single nation or faction but by an obscure, long-term agenda that often involves manipulating others for his own ends. He is calculating, patient, and demonstrates a fluid moral code, appearing to both aid and hinder the protagonists and their enemies with equal nonchalance. He seems to be motivated by a deep-seated weariness or curiosity, perhaps seeking a final end to his immortal existence or simply amusing himself by orchestrating the conflicts of mortals and poets.

Within the story, Saint-Germain serves as a pivotal catalyst who operates from the shadows. He is initially introduced as a mysterious prisoner who is clearly capable of escaping at any moment but chooses to wait for the right opportunity. He is associated with the Duc d'Orléans and is a high-ranking practitioner of the Psalms, the series' system of magic that allows for necromancy and the summoning of demonic entities known as poems. His role is that of a puppet master and a wild card; he provides crucial information, grants power to others on both sides of the conflict, and intervenes directly at key moments to ensure the continuation of his own inscrutable plans.

Saint-Germain's key relationships are defined by manipulation and a strange form of patronage. He meets with the Marquise de Pompadour, revealing that he visited her twenty years in the past and accurately predicted her rise to power, and offers her a magical ring that can grant a wish at a terrible price. In a more significant act, he approaches the poet Emma after her twin sister is killed. He banishes her master, Roble, and grants Emma a powerful new poem, which embodies the soul of her dead sister, effectively making her a seventh-rank poet while also instructing her to continue following Roble's commands. This act places a powerful agent on both sides of the war between the poets and the French crown, demonstrating his desire to perpetuate the conflict. He is also known to associate with the Count of Cagliostro, another infamous historical figure associated with the occult.

Throughout the story, Saint-Germain's character is developed by gradually revealing the terrifying extent of his abilities rather than his personal history. He survives what should be fatal encounters with ease. When confronted by the combined power of Queen Marie and Maximilien Robespierre, he is seemingly defeated but simply retreats to his hideout. Even when betrayed and crushed by rocks, he survives and undergoes a monstrous transformation into a gargoyle, ultimately requiring the combined efforts of King Louis XV and D'Eon to be defeated. In the manga version, his role is even more prominent, where he is initially hired by the Marquise de Pompadour as a handsome and mysterious investigator, immediately drawing the suspicion of Lord Douglas.

Saint-Germain's notable abilities are vast and exceed those of nearly every other character. As a master of the Psalms, he wields immense magical power, able to read verses that summon and command powerful poems, which are demonic servants. His most distinctive and terrifying power is the apparent ability to split his consciousness and form into multiple beings simultaneously. He accomplishes this by transforming himself into a moth and a wasp; the moth flies to meet with Madame de Pompadour, appearing in a seemingly normal human form, while the wasp seeks out Emma, appearing before her to offer his contract. This demonstrates a form of omnipresence or bilocation that makes him nearly impossible to track or trap. He is also capable of surviving fatal injuries and physical destruction, transforming into monstrous forms like a gargoyle, further suggesting a state of immortality that he may ultimately wish to escape.