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The young boy screams while his skull is forcefully gripped, a large digit digging into his cheek as his father's powerful palm grasps him by the throat. This moment from The Sacrifice of Isaac visits the Florentine museum, evoking unease through the artist's chilling rendition of the tormented youth from the scriptural narrative. The painting appears as if Abraham, commanded by the Divine to kill his son, could snap his neck with a solitary twist. Yet the father's chosen approach involves the metallic grey blade he holds in his other palm, prepared to cut Isaac's neck. One certain aspect stands out – whomever posed as Isaac for this breathtaking work demonstrated extraordinary acting skill. There exists not just fear, surprise and pleading in his darkened gaze but also deep grief that a protector could abandon him so completely.

The artist took a well-known biblical tale and transformed it so fresh and visceral that its terrors appeared to unfold directly in view of the viewer

Standing before the painting, viewers recognize this as a actual countenance, an accurate record of a adolescent subject, because the same boy – recognizable by his disheveled locks and nearly black eyes – features in several other works by the master. In each instance, that highly emotional face dominates the scene. In Youth With a Ram, he peers mischievously from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his dark feathery appendages demonic, a naked child creating riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a London museum, represents one of the most discomfiting masterpieces ever created. Observers feel completely unsettled looking at it. The god of love, whose arrows inspire people with frequently painful longing, is portrayed as a very real, brightly lit unclothed figure, straddling toppled-over objects that include musical devices, a music score, plate armour and an builder's ruler. This heap of possessions resembles, deliberately, the geometric and architectural equipment strewn across the floor in the German master's engraving Melencolia I – save here, the melancholic mess is caused by this smirking deity and the mayhem he can unleash.

"Love sees not with the vision, but with the soul, / And therefore is feathered Love painted sightless," wrote Shakespeare, shortly before this painting was produced around the early 1600s. But the painter's god is not unseeing. He stares directly at you. That countenance – sardonic and rosy-cheeked, staring with brazen assurance as he struts naked – is the identical one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his multiple portrayals of the same distinctive-appearing kid in the Eternal City at the start of the 17th century, he was the most acclaimed religious painter in a city enflamed by religious revival. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could adopt a scriptural narrative that had been portrayed numerous times before and render it so new, so unfiltered and physical that the terror seemed to be happening immediately before the spectator.

However there was a different aspect to the artist, evident as quickly as he came in the capital in the winter that ended 1592, as a painter in his initial 20s with no teacher or patron in the urban center, just talent and boldness. Most of the paintings with which he caught the holy city's eye were everything but devout. What could be the absolute first resides in the UK's National Gallery. A young man parts his crimson mouth in a yell of pain: while reaching out his filthy digits for a cherry, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's gloomy chamber reflected in the murky liquid of the glass container.

The adolescent wears a pink blossom in his coiffure – a symbol of the sex trade in Renaissance art. Venetian artists such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a painting lost in the WWII but documented through photographs, Caravaggio portrayed a renowned female courtesan, clutching a posy to her chest. The meaning of all these floral indicators is obvious: sex for purchase.

How are we to make of the artist's erotic portrayals of youths – and of one adolescent in particular? It is a inquiry that has divided his interpreters ever since he achieved widespread recognition in the 1980s. The complex historical truth is that the painter was not the homosexual icon that, for example, Derek Jarman presented on screen in his 1986 film about the artist, nor so entirely pious that, as some artistic historians unbelievably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early works do make explicit erotic suggestions, or including propositions. It's as if Caravaggio, then a destitute youthful artist, aligned with Rome's prostitutes, selling himself to live. In the Florentine gallery, with this idea in consideration, observers might turn to another initial work, the sixteenth-century masterpiece the god of wine, in which the god of alcohol stares calmly at the spectator as he starts to untie the dark ribbon of his garment.

A few annums after Bacchus, what could have motivated Caravaggio to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was at last growing nearly established with important church commissions? This unholy non-Christian god revives the erotic challenges of his initial works but in a more intense, unsettling way. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A British traveller viewed the painting in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Francesco.

The artist had been dead for about 40 annums when this account was documented.