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A young boy cries out as his skull is firmly held, a massive thumb pressing into his face as his father's mighty palm holds him by the neck. This moment from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through the artist's chilling rendition of the suffering youth from the biblical narrative. The painting seems as if the patriarch, commanded by God to sacrifice his son, could break his neck with a single twist. Yet the father's preferred approach involves the silvery steel blade he holds in his remaining palm, prepared to cut Isaac's throat. One definite aspect remains – whoever modeled as the sacrifice for this astonishing work demonstrated remarkable expressive ability. There exists not only dread, shock and begging in his darkened gaze but also deep sorrow that a guardian could abandon him so completely.

He adopted a familiar scriptural tale and made it so vibrant and visceral that its horrors seemed to unfold directly in view of the viewer

Standing before the artwork, viewers identify this as a real countenance, an accurate record of a adolescent subject, because the same boy – identifiable by his tousled hair and almost black pupils – features in two other paintings by the master. In every case, that highly expressive visage dominates the scene. In Youth With a Ram, he peers mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black plumed appendages sinister, a naked child running chaos in a well-to-do dwelling.

Amor Vincit Omnia, currently exhibited at a London gallery, represents one of the most discomfiting artworks ever created. Viewers feel totally disoriented gazing at it. The god of love, whose arrows fill people with often agonizing longing, is portrayed as a very real, vividly illuminated unclothed figure, standing over overturned items that include stringed devices, a music score, plate armour and an builder's T-square. This pile of possessions echoes, intentionally, the mathematical and architectural gear scattered across the floor in Albrecht Dürer's print Melencolia I – save in this case, the melancholic disorder is caused by this grinning Cupid and the turmoil he can unleash.

"Love sees not with the eyes, but with the mind, / And thus is winged Cupid painted sightless," wrote Shakespeare, shortly before this painting was produced around 1601. But the painter's Cupid is not unseeing. He stares directly at you. That countenance – ironic and rosy-faced, staring with bold confidence as he struts unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his multiple images of the same distinctive-looking youth in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred artist in a city ignited by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could take a scriptural story that had been depicted many occasions previously and make it so new, so raw and physical that the terror appeared to be occurring immediately in front of you.

However there was another side to Caravaggio, evident as quickly as he came in the capital in the cold season that concluded 1592, as a painter in his initial 20s with no mentor or supporter in the city, just talent and audacity. The majority of the works with which he captured the holy metropolis's eye were anything but devout. That may be the very first hangs in the UK's art museum. A youth parts his crimson mouth in a yell of agony: while stretching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see the painter's dismal room mirrored in the cloudy waters of the glass container.

The adolescent wears a pink blossom in his coiffure – a symbol of the erotic trade in Renaissance painting. Northern Italian painters such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a painting lost in the WWII but documented through photographs, Caravaggio portrayed a renowned woman prostitute, holding a posy to her bosom. The meaning of all these botanical signifiers is clear: intimacy for purchase.

What are we to interpret of the artist's erotic portrayals of youths – and of a particular adolescent in specific? It is a question that has split his interpreters ever since he gained mega-fame in the twentieth century. The complicated historical reality is that the painter was not the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century film about the artist, nor so completely pious that, as certain artistic scholars improbably claim, his Youth Holding Fruit is actually a portrait of Christ.

His early paintings indeed make explicit erotic implications, or including propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's prostitutes, selling himself to live. In the Florentine gallery, with this idea in consideration, observers might look to an additional initial work, the 1596 masterwork Bacchus, in which the deity of wine gazes calmly at you as he starts to untie the dark sash of his robe.

A several years following the wine deity, what could have driven the artist to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally becoming nearly established with important ecclesiastical projects? This profane pagan god resurrects the erotic provocations of his early works but in a more intense, uneasy way. Fifty years afterwards, its secret seemed clear: it was a representation of Caravaggio's companion. A British traveller saw Victorious Cupid in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this adolescent was Francesco.

The artist had been deceased for about forty years when this story was recorded.