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A young lad screams as his head is firmly held, a large digit digging into his face as his father's powerful palm holds him by the throat. This scene from Abraham's Sacrifice visits the Florentine museum, creating unease through the artist's harrowing rendition of the tormented child from the biblical narrative. It seems as if Abraham, instructed by God to sacrifice his son, could break his spinal column with a single turn. Yet the father's chosen approach involves the metallic steel blade he holds in his other hand, ready to slit the boy's neck. One definite aspect stands out – whoever posed as Isaac for this breathtaking work demonstrated extraordinary acting skill. There exists not only dread, shock and pleading in his shadowed eyes but also deep grief that a guardian could abandon him so utterly.

The artist adopted a well-known biblical tale and transformed it so fresh and visceral that its terrors seemed to happen right in front of the viewer

Viewing in front of the artwork, observers identify this as a actual face, an precise record of a young model, because the identical youth – identifiable by his tousled hair and almost black eyes – appears in two other works by the master. In every case, that highly expressive face commands the composition. In John the Baptist, he peers playfully from the shadows while embracing a lamb. In Victorious Cupid, he grins with a hardness learned on Rome's streets, his black plumed wings sinister, a unclothed adolescent running chaos in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a British museum, constitutes one of the most discomfiting artworks ever painted. Observers feel completely disoriented gazing at it. The god of love, whose arrows fill people with frequently painful longing, is shown as a very tangible, brightly lit nude form, straddling toppled-over objects that include stringed instruments, a music score, metal armor and an builder's ruler. This heap of items echoes, deliberately, the geometric and construction gear strewn across the ground in Albrecht Dürer's engraving Melencolia I – save here, the melancholic mess is caused by this grinning Cupid and the turmoil he can unleash.

"Love looks not with the vision, but with the soul, / And therefore is winged Cupid depicted blind," penned Shakespeare, shortly before this work was created around 1601. But Caravaggio's Cupid is not unseeing. He stares directly at the observer. That face – sardonic and ruddy-faced, staring with bold assurance as he struts unclothed – is the identical one that screams in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the identical distinctive-looking youth in Rome at the dawn of the 17th century, he was the most celebrated sacred artist in a city enflamed by religious revival. The Sacrifice of Isaac reveals why he was sought to adorn churches: he could adopt a biblical narrative that had been portrayed many times before and render it so new, so unfiltered and visceral that the horror appeared to be occurring directly in front of the spectator.

Yet there existed another aspect to Caravaggio, evident as soon as he came in Rome in the winter that ended the sixteenth century, as a painter in his initial 20s with no teacher or supporter in the urban center, only skill and boldness. Most of the paintings with which he captured the sacred metropolis's eye were everything but devout. That could be the absolute earliest hangs in London's art museum. A young man parts his red mouth in a yell of pain: while stretching out his filthy digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can discern Caravaggio's gloomy chamber reflected in the cloudy waters of the transparent vase.

The adolescent sports a rose-colored flower in his hair – a symbol of the erotic commerce in Renaissance painting. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans holding flowers and, in a painting destroyed in the second world war but documented through photographs, the master portrayed a renowned female courtesan, holding a bouquet to her chest. The meaning of all these botanical indicators is obvious: intimacy for sale.

How are we to make of Caravaggio's erotic portrayals of boys – and of a particular boy in specific? It is a question that has divided his commentators ever since he gained widespread recognition in the twentieth century. The complex past truth is that the painter was not the queer icon that, for example, the filmmaker presented on screen in his twentieth-century film Caravaggio, nor so entirely devout that, as certain artistic historians unbelievably claim, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early paintings do make explicit erotic implications, or including propositions. It's as if the painter, then a destitute youthful artist, identified with Rome's prostitutes, selling himself to survive. In the Uffizi, with this idea in mind, observers might turn to another early work, the 1596 masterpiece Bacchus, in which the god of alcohol stares coolly at the spectator as he begins to untie the black ribbon of his garment.

A several years following the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was at last growing almost established with important church projects? This profane pagan god revives the erotic provocations of his initial paintings but in a more powerful, unsettling way. Fifty years later, its hidden meaning seemed obvious: it was a representation of the painter's companion. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] own boy or assistant that slept with him". The identity of this boy was Francesco.

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