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A youthful lad cries out as his head is firmly held, a massive thumb pressing into his face as his father's mighty hand holds him by the neck. That scene from Abraham's Sacrifice appears in the Florentine museum, creating unease through the artist's harrowing portrayal of the suffering child from the biblical narrative. The painting seems as if the patriarch, instructed by God to kill his son, could snap his neck with a single twist. However the father's chosen method involves the metallic steel blade he holds in his remaining hand, ready to slit the boy's throat. A definite element remains – whoever posed as Isaac for this astonishing piece displayed remarkable acting ability. There exists not just dread, surprise and pleading in his shadowed gaze but also profound grief that a protector could betray him so completely.

He adopted a familiar biblical tale and transformed it so vibrant and raw that its horrors seemed to happen right in front of the viewer

Standing in front of the artwork, viewers recognize this as a actual countenance, an accurate record of a adolescent subject, because the same boy – identifiable by his tousled locks and almost black eyes – features in several additional works by Caravaggio. In each case, that richly expressive face commands the composition. In Youth With a Ram, he gazes playfully from the shadows while embracing a ram. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his dark feathery wings sinister, a unclothed child running chaos in a affluent residence.

Amor Vincit Omnia, presently displayed at a London museum, constitutes one of the most embarrassing artworks ever painted. Viewers feel totally unsettled gazing at it. The god of love, whose arrows inspire people with often agonizing desire, is shown as a very tangible, brightly illuminated unclothed figure, straddling overturned items that include musical instruments, a musical manuscript, metal armor and an builder's ruler. This heap of possessions resembles, deliberately, the geometric and architectural equipment scattered across the ground in the German master's engraving Melancholy – except here, the melancholic mess is created by this smirking Cupid and the mayhem he can release.

"Affection sees not with the vision, but with the soul, / And therefore is feathered Cupid painted sightless," wrote Shakespeare, just before this work was created around the early 1600s. But Caravaggio's Cupid is not unseeing. He stares directly at you. That countenance – ironic and rosy-faced, staring with bold assurance as he struts unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his multiple portrayals of the same unusual-appearing kid in Rome at the start of the 17th century, he was the most acclaimed religious painter in a city ignited by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could take a scriptural narrative that had been depicted numerous times previously and render it so new, so raw and physical that the terror appeared to be occurring immediately in front of you.

However there existed a different side to the artist, evident as soon as he came in the capital in the winter that ended the sixteenth century, as a painter in his initial 20s with no teacher or supporter in the city, just skill and boldness. The majority of the paintings with which he caught the holy metropolis's attention were anything but holy. What could be the absolute earliest resides in London's art museum. A youth parts his red mouth in a yell of pain: while stretching out his filthy fingers for a cherry, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern Caravaggio's dismal chamber reflected in the cloudy waters of the glass vase.

The boy wears a pink flower in his hair – a emblem of the sex trade in Renaissance painting. Venetian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping flowers and, in a work lost in the second world war but documented through photographs, Caravaggio portrayed a renowned woman courtesan, holding a bouquet to her bosom. The message of all these floral indicators is obvious: sex for purchase.

What are we to interpret of Caravaggio's erotic portrayals of boys – and of one boy in specific? It is a question that has divided his commentators ever since he achieved widespread recognition in the 1980s. The complex past reality is that the artist was not the homosexual icon that, for instance, the filmmaker put on film in his twentieth-century film Caravaggio, nor so entirely devout that, as certain art historians unbelievably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works do make explicit erotic implications, or even offers. It's as if Caravaggio, then a destitute young artist, identified with the city's sex workers, offering himself to live. In the Florentine gallery, with this thought in mind, observers might turn to an additional early work, the 1596 masterwork Bacchus, in which the deity of alcohol stares coolly at the spectator as he begins to untie the dark ribbon of his robe.

A few years after Bacchus, what could have motivated Caravaggio to paint Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last becoming almost respectable with prestigious church commissions? This profane pagan deity revives the sexual challenges of his initial works but in a increasingly intense, uneasy way. Fifty years afterwards, its secret seemed clear: it was a portrait of the painter's lover. A English visitor saw Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The name of this boy was Cecco.

The painter had been dead for about 40 annums when this story was documented.