Who exactly was the dark-feathered deity of love? What secrets this masterpiece reveals about the rogue genius

A youthful lad screams while his skull is forcefully gripped, a large thumb pressing into his face as his parent's powerful palm grasps him by the throat. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through Caravaggio's chilling portrayal of the suffering child from the biblical narrative. It appears as if Abraham, commanded by God to sacrifice his offspring, could snap his spinal column with a single twist. Yet Abraham's preferred method involves the silvery grey knife he grips in his remaining palm, ready to slit the boy's neck. A certain element stands out – whomever modeled as Isaac for this breathtaking work demonstrated extraordinary acting skill. There exists not only dread, shock and begging in his darkened gaze but also profound grief that a protector could abandon him so completely.

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

Standing before the artwork, viewers recognize this as a actual face, an accurate depiction of a young subject, because the same boy – identifiable by his disheveled locks and nearly dark pupils – appears in several additional works by Caravaggio. In every instance, that highly emotional visage dominates the scene. In Youth With a Ram, he peers playfully from the darkness while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on the city's streets, his dark feathery wings sinister, a naked child running riot in a affluent residence.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most embarrassing masterpieces ever painted. Viewers feel totally disoriented looking at it. Cupid, whose arrows fill people with often agonizing desire, is portrayed as a very real, vividly lit unclothed form, standing over overturned objects that comprise musical instruments, a musical score, metal armor and an architect's T-square. This heap of possessions echoes, intentionally, the mathematical and architectural gear strewn across the ground in the German master's engraving Melencolia I – save in this case, the melancholic mess is caused by this smirking deity and the turmoil he can unleash.

"Affection looks not with the vision, but with the soul, / And therefore is winged Cupid depicted blind," wrote the Bard, shortly before this painting was produced around 1601. But the painter's Cupid is not blind. He gazes directly at the observer. That face – ironic and ruddy-cheeked, looking with bold assurance as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three portrayals of the identical unusual-looking kid in Rome at the start of the 17th century, he was the most acclaimed religious artist in a city enflamed by religious revival. Abraham's Offering reveals why he was sought to decorate churches: he could take a scriptural story that had been portrayed many times previously and make it so fresh, so unfiltered and visceral that the terror seemed to be occurring immediately in front of you.

Yet there existed another side to the artist, evident as quickly as he arrived in Rome in the winter that ended 1592, as a painter in his initial twenties with no mentor or patron in the city, only skill and boldness. The majority of the works with which he captured the holy metropolis's eye were everything but holy. What may be the absolute earliest resides in the UK's National Gallery. A young man parts his red lips in a scream of pain: while reaching out his dirty fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can discern the painter's dismal room reflected in the murky waters of the transparent vase.

The boy wears a rose-colored flower in his coiffure – a symbol of the erotic trade in early modern art. Northern Italian painters such as Tiziano and Jacopo Palma depicted prostitutes holding flowers and, in a work lost in the WWII but documented through images, Caravaggio represented a renowned female prostitute, clutching a bouquet to her chest. The message of all these floral indicators is clear: sex for purchase.

What are we to make of Caravaggio's sensual depictions of youths – and of a particular adolescent in particular? It is a inquiry that has split his commentators since he gained widespread recognition in the 1980s. The complex past truth is that the artist was not the queer hero that, for instance, the filmmaker presented on film in his twentieth-century film about the artist, nor so entirely devout that, as some artistic scholars unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His initial paintings indeed make overt erotic suggestions, or including propositions. It's as if Caravaggio, then a destitute young artist, aligned with the city's sex workers, offering himself to live. In the Florentine gallery, with this thought in consideration, observers might look to another initial work, the 1596 masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he begins to untie the black sash of his garment.

A several years after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the art patron the nobleman, when he was finally becoming almost established with prestigious church projects? This profane non-Christian deity resurrects the erotic provocations of his initial works but in a increasingly powerful, unsettling way. Fifty years afterwards, its hidden meaning seemed obvious: it was a representation of Caravaggio's lover. A English visitor saw Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this adolescent was Cecco.

The artist had been dead for about forty years when this account was recorded.