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A young lad cries out while his skull is forcefully gripped, a large thumb pressing into his face as his father's powerful palm grasps him by the neck. That scene from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through the artist's harrowing portrayal of the tormented youth from the biblical narrative. It seems as if the patriarch, instructed by the Divine to kill his son, could snap his neck with a single turn. Yet the father's chosen approach involves the silvery grey blade he grips in his remaining palm, prepared to cut the boy's neck. One certain aspect stands out – whoever posed as the sacrifice for this astonishing work demonstrated remarkable acting ability. Within exists not only dread, surprise and begging in his darkened gaze but additionally profound sorrow that a guardian could abandon him so completely.

He adopted a familiar scriptural story and made it so fresh and visceral that its horrors appeared to happen right in view of the viewer

Standing in front of the painting, viewers recognize this as a real countenance, an accurate record of a young model, because the identical youth – identifiable by his tousled locks and almost dark pupils – features in two other works by Caravaggio. In each case, that richly emotional face dominates the composition. In Youth With a Ram, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his dark feathery wings demonic, a naked child running riot in a well-to-do residence.

Amor Vincit Omnia, presently displayed at a British museum, constitutes one of the most embarrassing masterpieces ever created. Viewers feel completely unsettled gazing at it. Cupid, whose arrows inspire people with often agonizing desire, is portrayed as a extremely tangible, vividly illuminated nude figure, straddling toppled-over objects that comprise musical devices, a musical score, metal armour and an builder's T-square. This pile of possessions resembles, intentionally, the mathematical and construction equipment scattered across the ground in Albrecht Dürer's print Melencolia I – save in this case, the melancholic mess is created by this grinning deity and the turmoil he can unleash.

"Affection looks not with the vision, but with the mind, / And thus is winged Cupid painted blind," penned the Bard, shortly before this painting was produced around 1601. But Caravaggio's Cupid is not blind. He gazes straight at you. That countenance – ironic and rosy-cheeked, staring with bold confidence as he struts naked – is the identical one that shrieks in fear in The Sacrifice of Isaac.

As the Italian master painted his multiple portrayals of the same unusual-appearing youth in the Eternal City at the dawn of the 17th century, he was the highly celebrated sacred artist in a metropolis ignited by religious renewal. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been depicted numerous times before and make it so new, so raw and visceral that the terror appeared to be occurring directly before the spectator.

Yet there existed another side to Caravaggio, evident as quickly as he arrived in the capital in the cold season that ended 1592, as a artist in his initial twenties with no mentor or supporter in the urban center, just talent and audacity. Most of the works with which he captured the holy metropolis's eye were anything but holy. What may be the very earliest resides in London's art museum. A youth parts his red mouth in a yell of pain: while stretching out his filthy digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid poverty: viewers can discern Caravaggio's gloomy chamber reflected in the murky waters of the transparent container.

The adolescent wears a pink blossom in his hair – a symbol of the sex commerce in Renaissance painting. Northern Italian artists such as Titian and Palma Vecchio portrayed courtesans grasping flowers and, in a painting destroyed in the second world war but documented through photographs, Caravaggio portrayed a famous woman prostitute, clutching a posy to her chest. The message of all these botanical signifiers is obvious: intimacy for purchase.

How are we to make of Caravaggio's erotic portrayals of youths – and of a particular adolescent in particular? It is a question that has divided his commentators ever since he achieved mega-fame in the twentieth century. The complicated past reality is that the painter was neither the homosexual hero that, for instance, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so entirely pious that, as certain artistic scholars unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works indeed offer overt sexual implications, or including propositions. It's as if the painter, then a penniless youthful creator, aligned with Rome's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, viewers might turn to an additional initial creation, the sixteenth-century masterwork Bacchus, in which the deity of wine gazes coolly at the spectator as he starts to untie the dark sash of his garment.

A few years following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last growing almost established with prestigious ecclesiastical projects? This unholy pagan deity resurrects the erotic provocations of his initial works but in a increasingly intense, uneasy way. Half a century later, its hidden meaning seemed clear: it was a representation of the painter's companion. A English visitor viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or servant that slept with him". The identity of this adolescent was Cecco.

The painter had been dead for about forty years when this story was documented.