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The young lad cries out as his head is firmly held, a massive thumb pressing into his face as his father's mighty palm grasps him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through the artist's harrowing portrayal of the tormented child from the scriptural narrative. It seems as if the patriarch, instructed by the Divine to sacrifice his son, could break his neck with a single turn. Yet the father's preferred approach involves the metallic grey blade he grips in his other palm, ready to slit the boy's throat. A definite aspect remains – whoever modeled as the sacrifice for this astonishing work displayed remarkable acting skill. There exists not only fear, shock and begging in his darkened eyes but additionally profound sorrow that a guardian could abandon him so completely.

The artist took a familiar scriptural tale and transformed it so fresh and raw that its horrors appeared to unfold directly in front of you

Viewing in front of the artwork, observers recognize this as a real face, an accurate depiction of a young model, because the identical youth – recognizable by his disheveled hair and nearly dark eyes – appears in two additional works by Caravaggio. In each case, that richly emotional visage commands the scene. In John the Baptist, he peers playfully from the darkness while embracing a ram. In Victorious Cupid, he grins with a toughness acquired on the city's streets, his black plumed appendages sinister, a unclothed child creating riot in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a London museum, constitutes one of the most discomfiting artworks ever created. Viewers feel totally unsettled gazing at it. The god of love, whose arrows fill people with often agonizing longing, is shown as a very tangible, vividly lit unclothed figure, standing over overturned objects that comprise musical devices, a music score, metal armor and an architect's T-square. This heap of possessions resembles, deliberately, the geometric and architectural gear strewn across the ground in the German master's print Melencolia I – save in this case, the melancholic disorder is created by this grinning deity and the turmoil he can unleash.

"Affection sees not with the eyes, but with the soul, / And therefore is winged Love depicted blind," wrote Shakespeare, shortly before this work was created around 1601. But the painter's god is not blind. He gazes straight at the observer. That countenance – ironic and ruddy-cheeked, looking with brazen assurance as he poses unclothed – is the same one that shrieks in fear in The Sacrifice of Isaac.

As the Italian master painted his multiple portrayals of the same unusual-looking kid in Rome at the start of the 17th century, he was the most celebrated religious artist in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was commissioned to decorate churches: he could take a scriptural story that had been depicted numerous occasions previously and make it so new, so unfiltered and visceral that the terror appeared to be occurring immediately in front of you.

However there was a different side to Caravaggio, evident as soon as he came in Rome in the cold season that concluded the sixteenth century, as a painter in his initial twenties with no teacher or patron in the urban center, just talent and audacity. The majority of the works with which he captured the sacred city's eye were everything but devout. What could be the very first hangs in the UK's art museum. A young man parts his red lips in a scream of pain: while reaching out his dirty digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern Caravaggio's gloomy chamber reflected in the murky waters of the transparent vase.

The boy sports a pink blossom in his coiffure – a symbol of the sex trade in early modern painting. Venetian painters such as Titian and Jacopo Palma depicted courtesans holding blooms and, in a work lost in the second world war but known through photographs, Caravaggio represented a renowned female prostitute, clutching a bouquet to her chest. The message of all these botanical indicators is clear: intimacy for sale.

What are we to make of the artist's sensual depictions 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 historical truth is that the painter was not the queer icon that, for example, the filmmaker presented on screen in his twentieth-century film about the artist, nor so entirely devout that, as certain art scholars unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His initial paintings indeed offer overt sexual suggestions, or even offers. It's as if Caravaggio, then a penniless youthful artist, aligned with Rome's sex workers, selling himself to live. In the Florentine gallery, with this idea in mind, viewers might turn to another early work, the sixteenth-century masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he starts to untie the black ribbon of his robe.

A few years after the wine deity, what could have motivated the artist to create Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last growing almost respectable with prestigious church projects? This unholy pagan god revives the sexual challenges of his early works but in a more powerful, uneasy manner. Half a century later, its hidden meaning seemed obvious: it was a portrait of the painter's companion. A British traveller saw Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] owne youth or servant that slept with him". The identity of this adolescent was Francesco.

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