Who exactly was Caravaggio's black-winged deity of love? What insights that masterpiece uncovers about the rebellious artist

A young boy cries out while his skull is firmly held, a large digit digging into his cheek as his father's powerful hand grasps him by the neck. This scene from The Sacrifice of Isaac visits the Florentine museum, creating distress through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. The painting seems as if the patriarch, instructed by God to sacrifice his offspring, could snap his spinal column with a single turn. However the father's chosen method involves the silvery steel blade he holds in his remaining palm, prepared to cut Isaac's throat. A definite aspect stands out – whoever posed as the sacrifice for this breathtaking work displayed remarkable expressive skill. Within exists not just fear, shock and pleading in his darkened gaze but additionally profound sorrow that a protector could betray him so completely.

The artist adopted a well-known scriptural tale and transformed it so fresh and visceral that its terrors appeared to unfold directly in front of the viewer

Viewing before the painting, observers identify this as a real face, an precise depiction of a adolescent subject, because the same boy – identifiable by his tousled locks and almost dark eyes – appears in two additional works by Caravaggio. In every instance, that richly expressive visage commands the scene. In Youth With a Ram, he peers mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a hardness acquired on the city's alleys, his dark plumed wings demonic, a naked child running chaos in a well-to-do dwelling.

Amor Vincit Omnia, presently exhibited at a London museum, represents one of the most embarrassing artworks ever painted. Viewers feel completely disoriented gazing at it. Cupid, whose darts fill people with frequently agonizing desire, is portrayed as a extremely real, brightly illuminated unclothed figure, straddling toppled-over items that comprise musical instruments, a musical manuscript, metal armour and an builder's T-square. This pile of possessions resembles, deliberately, the mathematical and construction gear strewn across the floor in Albrecht Dürer's engraving Melancholy – except in this case, the melancholic disorder is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Cupid painted blind," wrote Shakespeare, just before this work was created around the early 1600s. But Caravaggio's god is not blind. He stares directly at the observer. That face – sardonic and rosy-cheeked, staring with brazen assurance as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three images of the identical unusual-looking kid in the Eternal City at the dawn of the seventeenth century, he was the highly celebrated sacred painter in a metropolis enflamed by religious revival. Abraham's Offering reveals why he was commissioned to decorate sanctuaries: he could adopt a scriptural narrative that had been depicted numerous times previously and render it so new, so unfiltered and visceral that the terror seemed to be happening directly before you.

Yet there existed a different side to Caravaggio, apparent as quickly as he came in the capital in the cold season that ended 1592, as a painter in his initial 20s with no teacher or supporter in the city, only talent and audacity. Most of the works with which he caught the holy city's attention were anything but holy. What could be the absolute earliest resides in the UK's art museum. A young man opens his crimson lips in a yell of agony: while reaching out his dirty fingers for a fruit, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern the painter's dismal chamber reflected in the murky liquid of the transparent container.

The boy wears a pink blossom in his hair – a emblem of the sex trade in early modern art. Northern Italian artists such as Titian and Palma Vecchio depicted courtesans grasping blooms and, in a work destroyed in the second world war but documented through images, the master portrayed a famous woman prostitute, holding a posy to her bosom. The meaning of all these floral signifiers is clear: sex for sale.

How are we to make of Caravaggio's erotic portrayals of youths – and of one boy in particular? It is a question that has split his interpreters since he achieved widespread recognition in the twentieth century. The complicated historical truth is that the artist was not the queer hero that, for instance, the filmmaker put on film in his twentieth-century film about the artist, nor so entirely pious that, as certain art historians unbelievably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works indeed make explicit erotic suggestions, or including offers. It's as if Caravaggio, then a destitute young creator, identified with the city's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, viewers might look to another initial work, the 1596 masterwork the god of wine, in which the deity of alcohol stares coolly at you as he starts to untie the dark sash of his garment.

A few annums after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the art patron the nobleman, when he was at last growing almost respectable with important ecclesiastical projects? This profane pagan deity revives the erotic challenges of his initial works but in a increasingly intense, uneasy manner. Half a century afterwards, its secret seemed obvious: it was a representation of Caravaggio's companion. A British traveller saw Victorious Cupid in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or servant that laid with him". The name of this adolescent was Francesco.

The artist had been deceased for about 40 annums when this story was documented.