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The young boy screams while his head is firmly gripped, a large thumb pressing into his cheek as his father's mighty hand grasps him by the neck. This moment from Abraham's Sacrifice visits the Florentine museum, creating unease through the artist's chilling rendition of the suffering youth from the biblical narrative. The painting appears as if Abraham, commanded by God to sacrifice his offspring, could snap his neck with a solitary twist. However the father's chosen approach involves the metallic steel blade he grips in his other palm, ready to slit the boy's neck. A definite element remains – whoever posed as the sacrifice for this breathtaking piece demonstrated extraordinary expressive skill. There exists not only dread, surprise and begging in his shadowed gaze but also deep grief that a protector could abandon him so completely.

The artist adopted a well-known scriptural story and made it so fresh and visceral that its terrors appeared to happen right in front of you

Standing before the artwork, viewers recognize this as a real countenance, an accurate record of a young subject, because the same youth – identifiable by his disheveled locks and nearly dark pupils – features in several other works by Caravaggio. In each case, that highly expressive visage commands the scene. In Youth With a Ram, he gazes mischievously from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a hardness learned on the city's streets, his black feathery appendages demonic, a naked child creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most embarrassing masterpieces ever created. Observers feel completely disoriented looking at it. Cupid, whose arrows fill people with often painful longing, is portrayed as a extremely tangible, brightly illuminated unclothed figure, standing over overturned objects that include stringed instruments, a music score, plate armour and an builder's T-square. This heap of items resembles, intentionally, the mathematical and architectural equipment scattered across the ground in the German master's engraving Melencolia I – save here, the melancholic mess is caused by this grinning Cupid and the mayhem he can release.

"Affection looks not with the vision, but with the soul, / And therefore is winged Love depicted sightless," penned the Bard, just prior to this painting was produced around 1601. But the painter's god is not unseeing. He stares directly at you. That countenance – sardonic and ruddy-faced, staring with bold confidence as he struts naked – is the same one that screams in fear 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 start of the 17th century, he was the most acclaimed religious artist in a metropolis ignited by religious renewal. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could adopt a biblical story that had been portrayed numerous occasions before and make it so new, so unfiltered and visceral that the terror seemed to be happening immediately in front of you.

Yet there existed another side to Caravaggio, apparent as quickly as he came in Rome in the winter that ended 1592, as a painter in his initial twenties with no mentor or supporter in the urban center, just talent and audacity. The majority of the works with which he captured the sacred metropolis's attention were anything but holy. That could be the absolute first resides in London's National Gallery. A young man parts his crimson lips in a scream of pain: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern Caravaggio's dismal chamber mirrored in the cloudy waters of the glass container.

The adolescent wears a pink flower in his hair – a emblem of the erotic trade in early modern painting. Venetian artists such as Titian and Palma Vecchio depicted courtesans grasping blooms and, in a work destroyed in the second world war but known through images, Caravaggio portrayed a famous woman courtesan, holding a posy to her chest. The message of all these floral indicators is obvious: intimacy for sale.

What are we to make of Caravaggio's sensual depictions of youths – and of a particular adolescent in particular? It is a question that has split his interpreters since he achieved widespread recognition in the 1980s. The complex past truth is that the artist was not the queer hero that, for instance, Derek Jarman put on film in his 1986 movie about the artist, nor so completely pious that, as some artistic historians improbably assert, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early paintings do make overt sexual implications, or even offers. It's as if Caravaggio, then a destitute young creator, identified with Rome's prostitutes, selling himself to live. In the Florentine gallery, with this thought in consideration, viewers might turn to an additional early creation, the 1596 masterpiece Bacchus, in which the deity of alcohol stares coolly at the spectator as he begins to untie the black sash of his garment.

A several annums after the wine deity, what could have driven the artist to paint Amor Vincit Omnia for the art collector the nobleman, when he was finally growing almost respectable with important church projects? This profane pagan deity revives the erotic provocations of his early works but in a more intense, unsettling way. Half a century afterwards, its hidden meaning seemed clear: it was a portrait of the painter's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The name of this adolescent was Francesco.

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