Who was the dark-feathered deity of desire? The secrets that masterwork uncovers about the rogue artist

The youthful boy cries out as his head is firmly held, a large digit digging into his cheek as his father's mighty palm holds him by the neck. That moment from Abraham's Sacrifice visits the Florentine museum, evoking unease through Caravaggio's chilling portrayal of the suffering youth from the scriptural narrative. It appears as if Abraham, instructed by the Divine to kill his offspring, could break his neck with a solitary turn. Yet the father's preferred approach involves the silvery grey blade he holds in his remaining hand, prepared to slit the boy's throat. A certain aspect remains – whoever posed as Isaac for this breathtaking work displayed remarkable acting ability. Within exists not only dread, shock and begging in his darkened eyes but also profound sorrow that a guardian could betray him so utterly.

He adopted a familiar scriptural tale and made it so fresh and visceral that its terrors seemed to happen right in front of the viewer

Standing in front of the artwork, viewers recognize this as a real countenance, an accurate depiction of a adolescent model, because the identical boy – recognizable by his tousled hair and nearly black eyes – appears in two other works by Caravaggio. In each instance, that highly expressive visage commands the composition. In John the Baptist, he gazes mischievously from the shadows while holding a ram. In Victorious Cupid, he grins with a toughness learned on Rome's streets, his black plumed appendages demonic, a unclothed adolescent creating riot in a affluent residence.

Amor Vincit Omnia, presently exhibited at a British museum, constitutes one of the most embarrassing masterpieces ever painted. Viewers feel totally unsettled looking at it. The god of love, whose arrows inspire people with often painful longing, is portrayed as a very real, vividly lit unclothed form, straddling toppled-over items that comprise musical devices, a musical score, metal armour and an builder's ruler. This heap of items echoes, deliberately, the geometric and construction gear strewn across the floor in the German master's print Melencolia I – save here, the gloomy disorder is caused by this grinning deity and the turmoil he can release.

"Affection looks not with the eyes, but with the soul, / And therefore is winged Love depicted sightless," penned the Bard, just before this painting was created around 1601. But the painter's Cupid is not blind. He stares directly at the observer. That countenance – sardonic and ruddy-cheeked, staring with bold confidence as he poses naked – is the same one that screams in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three portrayals of the same distinctive-looking youth in Rome at the dawn of the seventeenth century, he was the most celebrated sacred painter in a city enflamed by Catholic revival. Abraham's Offering reveals why he was commissioned to decorate churches: he could adopt a scriptural story that had been portrayed numerous occasions before and render it so new, so raw and visceral that the horror seemed to be occurring immediately before you.

Yet there existed a different side to Caravaggio, apparent as quickly as he arrived in the capital in the cold season that concluded 1592, as a painter in his initial 20s with no mentor or supporter in the urban center, only skill and audacity. Most of the paintings with which he captured the sacred city's attention were everything but devout. What could be the very first resides in London's art museum. A youth parts his crimson mouth in a scream of agony: while reaching out his dirty fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can discern Caravaggio's gloomy chamber mirrored in the cloudy liquid of the transparent vase.

The adolescent sports a pink flower in his hair – a symbol of the erotic trade in early modern art. Venetian artists such as Titian and Palma Vecchio depicted prostitutes grasping blooms and, in a work destroyed in the WWII but documented through images, the master portrayed a renowned woman courtesan, clutching a bouquet to her chest. The message of all these floral signifiers is obvious: intimacy for sale.

What are we to make of the artist's sensual depictions of youths – and of one boy in specific? It is a question that has split his commentators since he gained mega-fame in the 1980s. The complex historical reality is that the painter was neither the homosexual icon that, for example, Derek Jarman put on film in his 1986 movie Caravaggio, nor so entirely pious that, as certain artistic scholars unbelievably claim, his Youth Holding Fruit is in fact a portrait of Christ.

His initial paintings indeed offer explicit sexual suggestions, or even propositions. It's as if Caravaggio, then a penniless youthful artist, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in consideration, viewers might turn to another initial creation, the 1596 masterwork the god of wine, in which the deity of wine stares coolly at you as he starts to undo the dark ribbon of his garment.

A few years after Bacchus, what could have driven Caravaggio to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally becoming almost respectable with prestigious church commissions? This profane pagan god resurrects the erotic provocations of his early works but in a more intense, uneasy manner. Fifty years later, its secret seemed clear: it was a portrait of the painter's companion. A British visitor saw the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this boy was Francesco.

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