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The youthful lad cries out while his skull is forcefully held, a massive thumb digging into his cheek as his father's mighty palm grasps him by the neck. That scene from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through Caravaggio's chilling rendition of the tormented child from the biblical narrative. It appears as if Abraham, commanded by the Divine to sacrifice his son, could break his neck with a single twist. Yet Abraham's preferred approach involves the silvery steel blade he holds in his remaining hand, ready to slit the boy's throat. One certain element remains – whomever posed as the sacrifice for this astonishing work displayed remarkable acting skill. There exists not only fear, surprise and pleading in his darkened gaze but also profound grief that a protector could abandon him so utterly.

He adopted a well-known scriptural tale and transformed it so vibrant and visceral that its terrors seemed to unfold directly in view of the viewer

Viewing before the artwork, viewers identify this as a actual countenance, an accurate record of a adolescent model, because the same boy – identifiable by his tousled locks and nearly black pupils – features in several additional works by the master. In each case, that highly emotional visage dominates the scene. In Youth With a Ram, he peers playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's alleys, his dark feathery appendages sinister, a naked child creating riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British museum, represents one of the most discomfiting masterpieces ever created. Observers feel totally disoriented looking at it. The god of love, whose arrows fill people with often agonizing desire, is shown as a very tangible, brightly illuminated nude figure, straddling overturned objects that comprise stringed devices, a music manuscript, plate armour and an builder's T-square. This pile of possessions echoes, deliberately, the mathematical and construction gear scattered across the ground in Albrecht Dürer's engraving Melancholy – except here, the gloomy disorder is created by this grinning deity and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And therefore is winged Love painted blind," wrote the Bard, shortly prior to this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at the observer. That face – sardonic and ruddy-faced, staring with brazen confidence as he struts unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his three portrayals of the same distinctive-looking youth in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred painter in a metropolis enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could adopt a biblical narrative that had been portrayed numerous occasions before and make it so fresh, so raw and visceral that the terror appeared to be occurring immediately in front of the spectator.

However there was another side to Caravaggio, evident as quickly as he came in the capital in the cold season that ended 1592, as a artist in his initial 20s with no mentor or patron in the urban center, just skill and audacity. The majority of the paintings with which he captured the holy metropolis's attention were anything but devout. What could be the very first hangs in London's art museum. A young man opens his crimson lips in a scream of pain: while stretching out his dirty fingers for a fruit, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see Caravaggio's dismal chamber reflected in the cloudy waters of the glass container.

The adolescent wears a pink blossom in his hair – a symbol of the sex trade in early modern painting. Venetian artists such as Titian and Palma Vecchio portrayed prostitutes holding flowers and, in a painting destroyed in the second world war but known through photographs, the master portrayed a famous woman prostitute, clutching a posy to her bosom. The meaning of all these botanical indicators is clear: sex for purchase.

What are we to make of Caravaggio's erotic depictions of boys – and of a particular adolescent in specific? It is a inquiry that has split his interpreters ever since he achieved mega-fame in the twentieth century. The complex past truth is that the painter was neither the queer icon that, for example, the filmmaker presented on film in his twentieth-century film about the artist, nor so completely pious that, as certain art scholars unbelievably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early paintings do make explicit sexual suggestions, or even offers. It's as if the painter, then a penniless youthful artist, identified with the city's sex workers, offering himself to live. In the Florentine gallery, with this thought in consideration, observers might look to another initial creation, the 1596 masterpiece Bacchus, in which the deity of wine gazes coolly at you as he starts to undo the black ribbon of his robe.

A several annums following the wine deity, what could have driven Caravaggio to paint Victorious Cupid for the art patron the nobleman, when he was finally growing almost respectable with prestigious ecclesiastical commissions? This unholy pagan deity resurrects the sexual provocations of his early paintings but in a increasingly powerful, uneasy way. Half a century later, its secret seemed clear: it was a representation of Caravaggio's lover. A English traveller viewed the painting in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] own boy or assistant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty annums when this account was recorded.