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A youthful boy screams as his head is firmly gripped, a large digit digging into his face as his father's powerful palm holds him by the neck. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, evoking unease through the artist's harrowing rendition of the tormented youth from the biblical narrative. It seems as if Abraham, instructed by God to sacrifice his offspring, could snap his neck with a solitary twist. However Abraham's chosen method involves the silvery steel knife he grips in his remaining palm, prepared to slit Isaac's neck. One certain aspect stands out – whomever modeled as the sacrifice for this breathtaking work demonstrated remarkable expressive skill. Within exists not only dread, shock and pleading in his shadowed eyes but also profound sorrow that a guardian could betray him so completely.

He adopted a well-known scriptural story and transformed it so fresh and raw that its terrors appeared to happen directly in front of you

Viewing in front of the artwork, viewers recognize this as a real face, an precise record of a young subject, because the same youth – recognizable by his tousled locks and almost dark eyes – features in several other works by Caravaggio. In each case, that highly emotional face dominates the scene. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a toughness learned on the city's streets, his black feathery wings demonic, a naked adolescent creating chaos in a well-to-do dwelling.

Amor Vincit Omnia, currently exhibited at a British museum, constitutes one of the most discomfiting artworks ever created. Observers feel completely unsettled looking at it. The god of love, whose darts fill people with often agonizing longing, is shown as a extremely tangible, brightly illuminated unclothed form, standing over overturned objects that comprise musical devices, a music score, plate armor and an architect's T-square. This pile of possessions resembles, intentionally, the geometric and construction gear scattered across the ground in the German master's engraving Melancholy – save in this case, the melancholic disorder is caused by this grinning deity and the mayhem he can release.

"Affection looks not with the eyes, but with the soul, / And thus is winged Cupid painted blind," penned the Bard, shortly before this painting was produced around the early 1600s. But Caravaggio's god is not unseeing. He stares straight at you. That countenance – ironic and rosy-faced, staring with bold assurance as he poses naked – is the same one that screams in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the identical distinctive-appearing youth in Rome at the start of the seventeenth century, he was the highly celebrated religious painter in a city enflamed by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted numerous times previously and render it so fresh, so unfiltered and visceral that the horror appeared to be occurring immediately in front of the spectator.

However there existed a different side to the artist, evident as soon as he arrived in the capital in the cold season that ended the sixteenth century, as a painter in his initial twenties with no teacher or supporter in the city, just skill and audacity. The majority of the paintings with which he caught the holy metropolis's eye were anything but devout. What could be the very first resides in the UK's art museum. A young man parts his red mouth in a scream of agony: while stretching out his filthy digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can see the painter's gloomy chamber mirrored in the murky liquid of the glass vase.

The boy wears a pink flower in his hair – a symbol of the sex trade in early modern painting. Northern Italian painters such as Tiziano and Jacopo Palma depicted prostitutes grasping flowers and, in a work lost in the second world war but documented through images, Caravaggio represented a renowned female courtesan, clutching a posy to her bosom. The meaning of all these floral signifiers is obvious: sex for purchase.

How are we to make of the artist's erotic portrayals of boys – and of a particular adolescent in specific? It is a inquiry that has divided his interpreters since he achieved widespread recognition in the 1980s. The complicated past truth is that the painter was neither the queer icon that, for instance, Derek Jarman presented on film in his 1986 film about the artist, nor so completely devout that, as some art scholars unbelievably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His early paintings indeed offer explicit erotic suggestions, or including propositions. It's as if the painter, then a destitute youthful creator, identified with the city's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, observers might turn to another initial work, the sixteenth-century masterpiece Bacchus, in which the deity of alcohol gazes calmly at you as he starts to untie the black ribbon of his robe.

A several years following the wine deity, what could have driven the artist to create Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally growing nearly respectable with important church projects? This unholy pagan god revives the sexual challenges of his initial works but in a increasingly intense, unsettling way. Fifty years later, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A English traveller saw the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] own boy or assistant that laid with him". The identity of this adolescent was Cecco.

The painter had been dead for about 40 years when this account was documented.