Who was the dark-feathered deity of love? What secrets that masterwork reveals about the rogue artist

A young boy cries out while his head is firmly gripped, a massive digit digging into his face as his father's mighty hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Florentine museum, creating unease through Caravaggio's chilling rendition of the tormented youth from the biblical account. It appears as if Abraham, instructed by God to kill his son, could snap his spinal column with a single turn. Yet Abraham's preferred approach involves the silvery grey knife he grips in his other palm, ready to cut the boy's throat. A certain aspect stands out – whoever modeled as the sacrifice for this astonishing work demonstrated extraordinary expressive ability. Within exists not only fear, surprise and pleading in his darkened eyes but also deep sorrow that a guardian could betray him so utterly.

The artist took a familiar scriptural story and made it so vibrant and raw that its terrors seemed to happen right in front of the viewer

Standing in front of the artwork, observers identify this as a real countenance, an accurate depiction of a adolescent subject, because the same boy – identifiable by his disheveled hair and almost black eyes – features in several additional paintings by the master. In each case, that richly emotional face commands the composition. In John the Baptist, he peers playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a hardness learned on the city's alleys, his dark plumed wings demonic, a naked adolescent running riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British gallery, represents one of the most embarrassing artworks ever created. Observers feel completely unsettled gazing at it. Cupid, whose arrows inspire people with frequently agonizing desire, is shown as a very real, vividly lit nude figure, straddling toppled-over objects that comprise stringed devices, a musical manuscript, metal armor and an architect's T-square. This pile of possessions resembles, deliberately, the mathematical and architectural gear scattered across the floor in Albrecht Dürer's print Melencolia I – save in this case, the melancholic disorder is caused by this grinning Cupid and the turmoil he can release.

"Affection sees not with the eyes, but with the soul, / And therefore is feathered Love painted sightless," wrote Shakespeare, just prior to this painting was produced around 1601. But the painter's god is not blind. He stares straight at you. That face – ironic and rosy-faced, looking with bold assurance as he poses naked – is the identical one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the same distinctive-looking kid in Rome at the start of the 17th century, he was the most acclaimed religious painter in a metropolis enflamed by Catholic renewal. Abraham's Offering reveals why he was commissioned to decorate churches: he could adopt a scriptural narrative that had been portrayed numerous times before and render it so fresh, so raw and physical that the terror seemed to be happening directly before the spectator.

However there existed another aspect to Caravaggio, apparent as soon as he came in the capital in the winter that concluded the sixteenth century, as a painter in his initial twenties with no mentor or patron in the city, only skill and boldness. Most of the paintings with which he caught the holy metropolis's attention were everything but holy. What could be the very earliest hangs in London's National Gallery. A young man parts his red lips in a yell of pain: while reaching out his filthy fingers for a cherry, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: viewers can discern the painter's gloomy room mirrored in the murky liquid of the transparent container.

The boy wears a pink blossom in his coiffure – a symbol of the erotic trade in early modern painting. Venetian painters such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a painting destroyed in the second world war but known through images, the master represented a renowned woman prostitute, holding a bouquet to her bosom. The meaning of all these botanical signifiers is clear: sex for purchase.

What are we to make of Caravaggio's erotic portrayals of boys – and of a particular boy in particular? It is a question that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complicated historical truth is that the painter was neither the queer hero that, for example, Derek Jarman put on screen in his twentieth-century movie about the artist, nor so entirely devout that, as some art historians unbelievably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works do offer overt sexual suggestions, or even offers. It's as if Caravaggio, then a penniless young creator, identified with the city's prostitutes, selling himself to survive. In the Florentine gallery, with this thought in mind, observers might look to another initial work, the sixteenth-century masterwork the god of wine, in which the god of wine stares calmly at the spectator as he begins to untie the dark sash of his robe.

A few years after Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was at last growing almost respectable with important ecclesiastical projects? This unholy pagan deity revives the erotic challenges of his initial works but in a increasingly intense, unsettling manner. Fifty years afterwards, its secret seemed clear: it was a portrait of Caravaggio's lover. A British traveller viewed the painting in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Francesco.

The painter had been deceased for about forty annums when this account was documented.