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The youthful lad cries out while his skull is forcefully held, a massive thumb pressing into his cheek as his father's powerful hand grasps him by the neck. That moment from Abraham's Sacrifice appears in the Florentine museum, creating unease through the artist's harrowing portrayal of the suffering child from the scriptural account. It seems as if the patriarch, commanded by God to sacrifice his son, could snap his neck with a solitary twist. Yet Abraham's preferred approach involves the silvery steel knife he grips in his other palm, ready to cut the boy's neck. One definite aspect remains – whomever posed as the sacrifice for this astonishing work demonstrated remarkable acting skill. Within exists not only dread, surprise and begging in his darkened gaze but also deep grief that a protector could betray him so utterly.

He adopted a well-known scriptural story and made it so vibrant and raw that its horrors seemed to unfold right in front of you

Standing in front of the artwork, viewers identify this as a actual face, an accurate record of a adolescent model, because the same boy – recognizable by his tousled locks and almost black eyes – appears in two other paintings by Caravaggio. In every instance, that highly expressive visage commands the scene. In John the Baptist, he peers mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's streets, his black feathery wings sinister, a unclothed child running chaos in a well-to-do residence.

Amor Vincit Omnia, currently exhibited at a British gallery, constitutes one of the most discomfiting masterpieces ever painted. Viewers feel totally unsettled looking at it. The god of love, whose arrows inspire people with often agonizing longing, is portrayed as a very real, vividly lit nude figure, standing over toppled-over items that comprise stringed devices, a musical manuscript, metal armour and an builder's T-square. This heap of possessions resembles, deliberately, the mathematical and architectural equipment strewn across the floor in the German master's print Melencolia I – except here, the gloomy mess is caused by this grinning deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted blind," wrote Shakespeare, just before this work was produced around 1601. But Caravaggio's god is not blind. He gazes directly at the observer. That face – ironic and ruddy-cheeked, looking with bold confidence as he struts unclothed – is the identical one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three portrayals of the same distinctive-looking kid in the Eternal City at the dawn of the 17th century, he was the highly celebrated sacred artist in a city enflamed by Catholic renewal. Abraham's Offering reveals why he was commissioned to decorate sanctuaries: he could adopt a scriptural narrative that had been portrayed many occasions previously and make it so new, so unfiltered and visceral that the terror seemed to be happening directly in front of the spectator.

Yet there was another side to the artist, apparent as soon as he came in Rome in the cold season that concluded the sixteenth century, as a artist in his early twenties with no teacher or patron in the city, just skill and audacity. Most of the paintings with which he captured the holy city's eye were everything but holy. What may be the very earliest resides in the UK's National Gallery. A young man parts his red mouth in a scream of pain: while stretching out his filthy digits for a cherry, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern the painter's gloomy room reflected in the cloudy liquid of the transparent container.

The boy sports a rose-colored blossom in his hair – a emblem of the sex trade in early modern art. Venetian painters such as Titian and Jacopo Palma portrayed prostitutes holding flowers and, in a work destroyed in the second world war but known through images, Caravaggio represented a famous female prostitute, clutching a bouquet to her chest. The message of all these floral signifiers is obvious: sex for sale.

How are we to make of Caravaggio's erotic depictions of youths – and of one adolescent in specific? It is a inquiry that has split his commentators since he achieved mega-fame in the twentieth century. The complicated past truth is that the artist was not the queer icon that, for example, Derek Jarman put on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as some artistic historians improbably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His initial works indeed offer explicit erotic suggestions, or even offers. It's as if the painter, then a penniless young artist, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in consideration, observers might look to another early work, the 1596 masterpiece Bacchus, in which the god of wine stares coolly at the spectator as he begins to undo the black sash of his garment.

A several years after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic collector the nobleman, when he was at last growing almost respectable with important church projects? This profane non-Christian god resurrects the sexual provocations of his early paintings but in a increasingly powerful, unsettling manner. Fifty years afterwards, its secret seemed clear: it was a representation of Caravaggio's lover. A English visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The name of this adolescent was Francesco.

The painter had been dead for about 40 years when this account was documented.