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The young boy cries out as his head is firmly held, a large thumb digging into his cheek as his father's powerful palm grasps him by the neck. This moment from The Sacrifice of Isaac visits the Florentine museum, creating distress through Caravaggio's harrowing rendition of the suffering youth from the biblical narrative. It appears as if the patriarch, commanded by the Divine to sacrifice his offspring, could break his spinal column with a solitary turn. However the father's chosen method involves the metallic grey knife he grips in his other palm, prepared to slit Isaac's neck. One definite aspect stands out – whoever posed as Isaac for this breathtaking work displayed remarkable expressive ability. There exists not only fear, shock and begging in his darkened eyes but additionally profound grief that a protector could abandon him so utterly.

He took a familiar biblical story and made it so vibrant and visceral that its terrors appeared to happen directly in front of the viewer

Standing before the artwork, viewers identify this as a real face, an precise record of a young model, because the same boy – recognizable by his tousled locks and almost dark eyes – appears in two additional works by Caravaggio. In each instance, that richly expressive face dominates the scene. In John the Baptist, he gazes playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his black feathery wings sinister, a unclothed adolescent creating chaos in a affluent residence.

Amor Vincit Omnia, currently displayed at a British museum, represents one of the most discomfiting artworks ever created. Viewers feel totally disoriented looking at it. Cupid, whose arrows fill people with often agonizing longing, is portrayed as a very tangible, brightly lit nude form, straddling overturned items that comprise stringed instruments, a music score, plate armour and an architect's ruler. This heap of possessions resembles, intentionally, the mathematical and architectural gear strewn across the ground in the German master's engraving Melancholy – except in this case, the gloomy disorder is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the eyes, but with the soul, / And therefore is winged Cupid painted sightless," wrote Shakespeare, shortly prior to this work was created around the early 1600s. But the painter's Cupid is not blind. He stares directly at you. That face – ironic and ruddy-cheeked, staring with brazen assurance as he struts unclothed – is the identical one that shrieks in terror in Abraham's Test.

When the Italian master created his three portrayals of the identical distinctive-appearing kid in Rome at the dawn of the 17th century, he was the most acclaimed religious painter in a city enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could take a scriptural story that had been portrayed many occasions previously and render it so fresh, so raw and physical that the horror seemed to be occurring immediately before you.

Yet there was another side to the artist, apparent as quickly as he arrived in Rome in the winter that ended 1592, as a artist in his initial 20s with no mentor or supporter in the urban center, just skill and audacity. Most of the works with which he caught the sacred metropolis's attention were everything but devout. What could be the absolute first hangs in London's National Gallery. A youth opens his crimson mouth in a scream of pain: while reaching out his dirty fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's gloomy chamber mirrored in the cloudy liquid of the glass container.

The boy wears a pink blossom in his hair – a symbol of the erotic commerce in early modern painting. Northern Italian painters such as Titian and Palma Vecchio portrayed courtesans holding flowers and, in a painting destroyed in the second world war but known through photographs, the master portrayed a renowned woman courtesan, holding a bouquet to her chest. The message of all these botanical signifiers is obvious: intimacy for purchase.

How are we to make of the artist's sensual depictions of boys – and of a particular adolescent in particular? It is a inquiry that has split his interpreters ever since he achieved widespread recognition in the 1980s. The complex past truth is that the painter was neither the homosexual icon that, for example, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so entirely devout that, as some art historians unbelievably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial works indeed make overt erotic implications, or including propositions. It's as if the painter, then a destitute youthful artist, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this idea in consideration, observers might look to another initial work, the sixteenth-century masterpiece the god of wine, in which the god of wine stares calmly at you as he starts to untie the black sash of his robe.

A several years after the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the art collector the nobleman, when he was at last growing almost established with prestigious church projects? This unholy non-Christian deity revives the sexual challenges of his initial paintings but in a more intense, uneasy way. Fifty years afterwards, its secret seemed obvious: it was a representation of Caravaggio's lover. A English traveller saw Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this boy was Francesco.

The painter had been dead for about 40 annums when this account was recorded.