What exactly was Caravaggio's dark-feathered god of desire? The secrets that masterpiece uncovers about the rogue artist

A young lad cries out while his head is forcefully gripped, a massive digit digging into his face as his parent's powerful palm grasps him by the neck. That moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's harrowing rendition of the tormented child from the biblical account. The painting appears as if Abraham, commanded by God to sacrifice his offspring, could break his spinal column with a single turn. Yet Abraham's chosen approach involves the metallic grey knife he holds in his remaining palm, prepared to slit Isaac's neck. A certain element remains – whoever posed as the sacrifice for this breathtaking work displayed extraordinary acting skill. Within exists not just fear, surprise and pleading in his darkened eyes but additionally deep grief that a protector could abandon him so completely.

He took a well-known biblical story and made it so fresh and visceral that its terrors appeared to unfold right in front of the viewer

Viewing in front of the painting, viewers recognize this as a real face, an precise record of a adolescent subject, because the identical boy – recognizable by his tousled hair and almost dark pupils – appears in several other works by the master. In every instance, that highly emotional face dominates the scene. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his black feathery appendages sinister, a unclothed child running riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British museum, represents one of the most embarrassing artworks ever painted. Viewers feel totally disoriented gazing at it. The god of love, whose darts fill people with often agonizing longing, is shown as a extremely real, brightly illuminated nude figure, standing over overturned items that comprise stringed devices, a music manuscript, plate armor and an architect's T-square. This pile of items resembles, intentionally, the geometric and architectural equipment strewn across the ground in Albrecht Dürer's print Melancholy – except in this case, the gloomy disorder is created by this grinning Cupid and the turmoil he can release.

"Love looks not with the vision, but with the mind, / And therefore is winged Love depicted sightless," wrote the Bard, just prior to this work was created around the early 1600s. But the painter's Cupid is not blind. He stares straight at the observer. That countenance – sardonic and rosy-faced, looking with bold assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the same distinctive-appearing youth in the Eternal City at the dawn of the seventeenth century, he was the highly acclaimed sacred painter in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could take a biblical narrative that had been portrayed numerous times before and make it so fresh, so raw and visceral that the terror seemed to be happening directly before the spectator.

However there was another side to Caravaggio, apparent as quickly as he arrived in the capital in the winter that ended the sixteenth century, as a artist in his initial 20s with no teacher or supporter in the urban center, only skill and audacity. The majority of the works with which he captured the holy city's eye were everything but holy. That could be the absolute earliest hangs in the UK's National Gallery. A young man opens his red lips in a yell of pain: while reaching out his filthy fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid squalor: observers can discern the painter's gloomy room reflected in the cloudy liquid of the glass vase.

The boy wears a rose-colored flower in his coiffure – a symbol of the sex trade in early modern art. Northern Italian artists such as Titian and Palma Vecchio depicted courtesans grasping blooms and, in a painting lost in the second world war but documented through photographs, the master represented a renowned female prostitute, holding a bouquet to her chest. The message of all these botanical signifiers is clear: sex for purchase.

How are we to make of Caravaggio's erotic depictions of youths – and of a particular boy in particular? It is a inquiry that has split his interpreters since he achieved widespread recognition in the twentieth century. The complicated historical truth is that the painter was neither the homosexual hero that, for instance, the filmmaker put on screen in his 1986 film Caravaggio, nor so entirely pious that, as certain art historians unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works indeed offer overt erotic implications, or including propositions. It's as if Caravaggio, then a penniless youthful artist, identified with Rome's prostitutes, offering himself to live. In the Uffizi, with this idea in consideration, observers might look to another initial work, the 1596 masterwork Bacchus, in which the deity of alcohol gazes calmly at you as he begins to untie the black ribbon of his robe.

A few years following Bacchus, what could have driven Caravaggio to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was finally becoming nearly respectable with prestigious ecclesiastical commissions? This profane non-Christian god resurrects the erotic provocations of his initial paintings but in a increasingly powerful, unsettling way. Fifty years afterwards, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A English visitor saw the painting in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this adolescent was Cecco.

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