Who was Caravaggio's black-winged deity of love? The secrets that masterwork reveals about the rogue genius

A young boy cries out as his skull is firmly gripped, a large digit pressing into his face as his parent's mighty hand holds him by the neck. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through the artist's harrowing portrayal of the tormented youth from the scriptural account. The painting seems as if the patriarch, instructed by the Divine to kill his son, could snap his neck with a solitary turn. However Abraham's preferred method involves the silvery grey knife he holds in his other palm, prepared to slit Isaac's neck. One certain element stands out – whomever posed as Isaac for this astonishing piece displayed remarkable expressive skill. There exists not only dread, shock and pleading in his shadowed gaze but additionally profound grief that a protector could betray him so utterly.

The artist adopted a familiar scriptural tale and made it so fresh and visceral that its horrors seemed to happen right in front of the viewer

Standing before the painting, viewers identify this as a real face, an precise record of a young model, because the identical boy – identifiable by his disheveled locks and almost black eyes – appears in two additional works by the master. In each case, that highly emotional visage commands the composition. In John the Baptist, he peers playfully from the shadows while holding a lamb. In Victorious Cupid, he grins with a toughness learned on Rome's streets, his black plumed wings sinister, a unclothed adolescent running chaos in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British museum, constitutes one of the most discomfiting masterpieces ever painted. Observers feel completely disoriented gazing at it. Cupid, whose darts inspire people with often painful longing, is shown as a very real, brightly illuminated unclothed form, standing over overturned items that comprise musical devices, a musical score, metal armour and an builder's ruler. This pile of items resembles, deliberately, the geometric and construction equipment strewn across the floor in Albrecht Dürer's engraving Melencolia I – except here, the melancholic disorder is created by this smirking deity and the turmoil he can unleash.

"Affection sees not with the eyes, but with the soul, / And therefore is winged Love painted blind," wrote the Bard, just prior to this painting was produced around the early 1600s. But the painter's Cupid is not unseeing. He stares straight at you. That face – ironic and rosy-faced, staring with brazen confidence as he poses naked – is the same one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the identical unusual-looking kid in Rome at the dawn of the seventeenth century, he was the most acclaimed religious artist in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was commissioned to decorate churches: he could adopt a biblical story that had been portrayed numerous occasions before and make it so fresh, so raw and physical that the terror seemed to be happening immediately before you.

Yet there was a different aspect to the artist, apparent as soon as he arrived in the capital in the winter that concluded 1592, as a artist in his initial twenties with no mentor or supporter in the city, just skill and audacity. Most of the paintings with which he caught the sacred metropolis's eye were everything but devout. That may be the absolute first hangs in London's art museum. A young man opens his crimson mouth in a scream of agony: while stretching out his filthy fingers for a cherry, he has rather been bitten. Youth Bitten by a Reptile is sensuality amid poverty: viewers can see Caravaggio's dismal room reflected in the murky waters of the glass vase.

The adolescent sports a pink flower in his hair – a symbol of the erotic trade in Renaissance art. Northern Italian artists such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a work destroyed in the WWII but documented through photographs, the master represented a renowned woman prostitute, holding a bouquet to her chest. The message of all these botanical signifiers is clear: sex for purchase.

What are we to make of Caravaggio's erotic depictions of youths – and of one boy in specific? It is a inquiry that has divided his commentators since he gained mega-fame in the twentieth century. The complicated historical truth is that the artist was neither the homosexual hero that, for instance, Derek Jarman put on film in his 1986 film Caravaggio, nor so entirely devout that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His initial paintings indeed offer overt erotic suggestions, or even propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's sex workers, selling himself to survive. In the Florentine gallery, with this thought in consideration, observers might look to an additional initial creation, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at you as he starts to undo the black sash of his garment.

A few years after Bacchus, what could have driven Caravaggio to create Victorious Cupid for the artistic patron the nobleman, when he was finally becoming almost respectable with important church commissions? This profane non-Christian deity resurrects the erotic provocations of his initial paintings but in a more intense, uneasy way. Fifty years afterwards, its secret seemed obvious: it was a representation of the painter's companion. A British visitor saw the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or servant that slept with him". The name of this adolescent was Francesco.

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