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A youthful boy cries out while his head is firmly gripped, a large digit pressing into his cheek as his parent's mighty palm grasps him by the neck. This moment from The Sacrifice of Isaac visits the Florentine museum, evoking unease through Caravaggio's harrowing rendition of the suffering youth from the biblical narrative. It seems as if Abraham, instructed by the Divine to kill his son, could break his neck with a solitary twist. Yet the father's chosen approach involves the metallic grey knife he holds in his remaining palm, ready to slit the boy's neck. A definite element remains – whomever posed as the sacrifice for this breathtaking work demonstrated remarkable acting ability. There exists not only fear, surprise and begging in his shadowed eyes but also deep sorrow that a protector could abandon him so utterly.

The artist adopted a familiar scriptural story and made it so fresh and raw that its terrors seemed to unfold right in view of the viewer

Viewing before the artwork, observers identify this as a real countenance, an accurate depiction of a young subject, because the same youth – recognizable by his disheveled locks and almost dark pupils – features in several additional works by Caravaggio. In every case, that highly emotional face commands the composition. In Youth With a Ram, he gazes mischievously from the darkness while embracing a ram. In Victorious Cupid, he smirks with a toughness acquired on the city's alleys, his black plumed appendages demonic, a unclothed adolescent running chaos in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a British museum, represents one of the most embarrassing artworks ever created. Observers feel totally unsettled looking at it. Cupid, whose darts fill people with often agonizing longing, is shown as a extremely tangible, vividly lit unclothed figure, standing over overturned items that comprise musical devices, a musical manuscript, metal armor and an builder's T-square. This heap of possessions resembles, deliberately, the mathematical and architectural gear scattered across the floor in the German master's engraving Melencolia I – save here, the melancholic disorder is created by this smirking Cupid and the turmoil he can unleash.

"Love sees not with the vision, but with the soul, / And therefore is feathered Love painted sightless," penned Shakespeare, shortly prior to this work was produced around 1601. But Caravaggio's god is not blind. He gazes directly at the observer. That countenance – ironic and ruddy-cheeked, staring with brazen confidence as he struts naked – is the same one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his multiple images of the identical distinctive-looking kid in the Eternal City at the start of the 17th century, he was the most acclaimed sacred artist in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been portrayed many times previously and make it so new, so raw and visceral that the terror seemed to be occurring directly before you.

Yet there was another side to the artist, evident as soon as he arrived in Rome in the cold season that ended the sixteenth century, as a painter in his early twenties with no mentor or patron in the city, only skill and audacity. Most of the works with which he caught the holy city's attention were everything but devout. That may be the very first resides in the UK's art museum. A young man parts his red mouth in a yell of agony: while reaching out his dirty fingers for a fruit, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see the painter's gloomy chamber mirrored in the murky waters of the transparent vase.

The boy sports a rose-colored flower in his hair – a emblem of the erotic trade in early modern painting. Northern Italian artists such as Tiziano and Palma Vecchio depicted prostitutes grasping blooms and, in a work destroyed in the WWII but documented through photographs, Caravaggio represented a renowned female courtesan, holding a posy to her bosom. The message of all these floral signifiers is clear: intimacy for purchase.

What are we to make of Caravaggio's erotic portrayals of boys – and of one adolescent in specific? It is a question that has divided his commentators since he achieved mega-fame in the 1980s. The complicated historical truth is that the artist was neither the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century movie about the artist, nor so completely pious that, as some art historians improbably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His initial works indeed offer overt sexual implications, or including offers. It's as if Caravaggio, then a destitute young artist, aligned with the city's sex workers, offering himself to survive. In the Uffizi, with this thought in mind, viewers might look to another initial work, the 1596 masterwork Bacchus, in which the god of alcohol stares coolly at the spectator as he starts to undo the dark ribbon of his garment.

A few years after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally becoming nearly respectable with prestigious ecclesiastical commissions? This profane pagan deity resurrects the sexual challenges of his early works but in a more powerful, uneasy manner. Half a century afterwards, its secret seemed obvious: it was a portrait of the painter's companion. A English visitor saw Victorious Cupid in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] own boy or assistant that laid with him". The name of this adolescent was Cecco.

The painter had been dead for about 40 years when this story was recorded.