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The young lad cries out as his head is firmly held, a massive thumb digging into his face as his father's mighty palm holds him by the neck. That scene from The Sacrifice of Isaac visits the Florentine museum, evoking unease through the artist's harrowing portrayal of the suffering child from the biblical account. The painting appears as if Abraham, commanded by God to sacrifice his offspring, could break his spinal column with a single twist. Yet the father's chosen method involves the metallic steel knife he holds in his remaining hand, prepared to slit the boy's throat. A certain aspect stands out – whomever posed as the sacrifice for this breathtaking piece displayed extraordinary expressive skill. Within exists not only fear, surprise and begging in his shadowed eyes but additionally profound sorrow that a guardian could betray him so completely.

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

Standing in front of the artwork, viewers recognize this as a actual face, an precise depiction of a young subject, because the identical boy – recognizable by his tousled locks and nearly black eyes – appears in two additional works by Caravaggio. In each case, that richly expressive visage dominates the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on the city's streets, his dark feathery appendages sinister, a unclothed child running chaos in a well-to-do dwelling.

Victorious Cupid, presently displayed at a British gallery, constitutes one of the most embarrassing artworks ever painted. Viewers feel completely disoriented looking at it. Cupid, whose arrows inspire people with often painful desire, is shown as a very tangible, brightly illuminated nude form, standing over overturned items that include stringed devices, a musical manuscript, metal armor and an builder's ruler. This pile of possessions echoes, intentionally, the geometric and architectural gear strewn across the ground in the German master's print Melencolia I – except in this case, the gloomy disorder is caused by this smirking deity and the turmoil he can release.

"Love sees not with the eyes, but with the mind, / And therefore is winged Cupid depicted sightless," penned the Bard, just prior to this painting was produced around 1601. But the painter's Cupid is not unseeing. He stares straight at you. That countenance – ironic and rosy-cheeked, staring with bold confidence as he poses naked – is the same one that screams in terror in The Sacrifice of Isaac.

As the Italian master painted his three portrayals of the same unusual-looking kid in the Eternal City at the dawn of the seventeenth century, he was the highly acclaimed sacred artist in a metropolis enflamed by Catholic renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been portrayed many times before and make it so fresh, so unfiltered and visceral that the horror seemed to be happening directly before you.

Yet there was another aspect to the artist, evident as quickly as he came in Rome in the winter that ended the sixteenth century, as a painter in his early twenties with no teacher or supporter in the city, just talent and audacity. Most of the paintings with which he caught the sacred metropolis's attention were anything but devout. That may be the absolute first resides in London's art museum. A young man opens his red mouth in a yell of agony: while reaching out his filthy fingers for a cherry, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: viewers can see the painter's gloomy room reflected in the cloudy liquid of the glass vase.

The boy wears a rose-colored flower in his hair – a symbol of the sex commerce in early modern painting. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a painting lost in the second world war but documented through photographs, the master portrayed a renowned female courtesan, holding a posy to her chest. The message of all these floral indicators is clear: intimacy for purchase.

What are we to interpret of Caravaggio's sensual portrayals of boys – and of a particular boy in specific? It is a inquiry that has split his commentators ever since he achieved mega-fame in the 1980s. The complex historical reality is that the artist was not the homosexual icon that, for instance, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so entirely pious that, as some art historians unbelievably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His early works do make overt sexual suggestions, or including propositions. It's as if the painter, then a penniless youthful creator, identified with the city's sex workers, offering himself to live. In the Uffizi, with this idea in mind, observers might look to another early creation, the sixteenth-century masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he begins to untie the black sash of his robe.

A few years after Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron the nobleman, when he was at last growing almost established with important church projects? This unholy non-Christian god revives the sexual provocations of his initial paintings but in a more powerful, unsettling way. Fifty years afterwards, its secret seemed obvious: it was a portrait of the painter's lover. A British visitor viewed Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or servant that laid with him". The identity of this boy was Cecco.

The artist had been deceased for about 40 annums when this story was documented.