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A young boy screams while his head is forcefully held, a massive digit pressing into his face as his father's powerful hand grasps him by the throat. That scene from The Sacrifice of Isaac appears in the Florentine museum, creating distress through the artist's chilling rendition of the tormented youth from the scriptural account. It appears as if Abraham, instructed by God to kill his offspring, could break his spinal column with a solitary turn. Yet the father's chosen approach involves the metallic grey knife he grips in his other hand, ready to slit the boy's neck. One definite aspect remains – whoever modeled as Isaac for this breathtaking piece demonstrated extraordinary expressive skill. Within exists not just fear, shock and begging in his darkened gaze but also profound sorrow that a protector could abandon him so utterly.

He adopted a well-known biblical story and made it so vibrant and visceral that its horrors seemed to unfold right in view of you

Viewing in front of the painting, observers recognize this as a real countenance, an accurate depiction of a young model, because the same youth – recognizable by his tousled locks and almost dark pupils – features in two other works by Caravaggio. In each case, that richly emotional visage commands the scene. In John the Baptist, he gazes playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on the city's streets, his black plumed wings sinister, a naked adolescent creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently exhibited at a London museum, constitutes one of the most embarrassing artworks ever created. Observers feel completely unsettled looking at it. Cupid, whose darts fill people with frequently painful desire, is shown as a extremely real, vividly lit nude form, straddling overturned objects that comprise stringed devices, a musical manuscript, plate armor and an builder's ruler. This heap of possessions resembles, intentionally, the geometric and construction equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – except in this case, the melancholic mess is created by this smirking deity and the turmoil he can release.

"Love sees not with the eyes, but with the soul, / And therefore is feathered Cupid painted sightless," penned Shakespeare, shortly before this painting was produced around the early 1600s. But the painter's Cupid is not blind. He stares straight at the observer. That countenance – ironic and ruddy-cheeked, looking with bold assurance as he poses naked – is the same one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his multiple images of the same unusual-appearing youth in Rome at the dawn of the 17th century, he was the highly acclaimed sacred painter in a city enflamed by religious renewal. The Sacrifice of Isaac reveals why he was sought to decorate churches: he could adopt a scriptural story that had been portrayed many occasions previously and make it so new, so unfiltered and visceral that the horror appeared to be occurring immediately before you.

Yet there was a different aspect to Caravaggio, evident as soon as he came in the capital in the cold season that ended the sixteenth century, as a artist in his initial twenties with no teacher or supporter in the urban center, only skill and audacity. Most of the paintings with which he captured the holy metropolis's eye were anything but holy. That may be the absolute earliest hangs in London's National Gallery. A young man parts his red lips in a scream of agony: while stretching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: observers can see the painter's gloomy chamber reflected in the cloudy liquid of the transparent container.

The adolescent sports a pink flower in his coiffure – a emblem of the sex commerce in Renaissance painting. Northern Italian painters such as Tiziano and Palma Vecchio depicted courtesans grasping blooms and, in a work destroyed in the second world war but known through images, the master portrayed a famous female courtesan, holding a posy to her chest. The meaning of all these botanical signifiers is clear: intimacy for purchase.

What are we to make of the artist's erotic depictions of youths – and of a particular boy in particular? It is a question that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complex past reality is that the painter was not the homosexual hero that, for instance, Derek Jarman put on film in his twentieth-century film about the artist, nor so entirely devout that, as some artistic scholars unbelievably claim, his Youth Holding Fruit is actually a likeness of Jesus.

His early paintings do offer overt sexual implications, or even offers. It's as if Caravaggio, then a penniless youthful creator, identified with Rome's sex workers, selling himself to live. In the Uffizi, with this idea in mind, observers might turn to an additional early creation, the sixteenth-century masterpiece the god of wine, in which the god of alcohol stares coolly at you as he starts to undo the dark sash of his garment.

A several years after Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was at last becoming almost established with important church projects? This profane non-Christian god resurrects the erotic challenges of his initial paintings but in a more intense, unsettling way. Half a century afterwards, its secret seemed obvious: it was a representation of Caravaggio's lover. A British visitor saw Victorious Cupid in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Francesco.

The painter had been dead for about forty annums when this story was recorded.