What exactly was the dark-feathered god of desire? What secrets that masterwork uncovers about the rebellious genius

A youthful lad cries out as his head is firmly held, a large digit digging into his face as his father's mighty palm holds him by the throat. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's chilling portrayal of the tormented child from the scriptural narrative. The painting seems as if Abraham, instructed by God to kill his son, could snap his spinal column with a solitary twist. However Abraham's preferred method involves the metallic grey knife he holds in his remaining palm, prepared to cut the boy's throat. One definite element stands out – whoever modeled as the sacrifice for this astonishing piece displayed remarkable acting skill. There exists not just fear, surprise and pleading in his darkened gaze but additionally deep grief that a guardian could abandon him so completely.

The artist took a familiar biblical tale and made it so vibrant and visceral that its horrors seemed to happen right in front of the viewer

Viewing before the painting, viewers recognize this as a real face, an precise record of a adolescent subject, because the same boy – identifiable by his disheveled hair and almost black pupils – features in two other paintings by the master. In every instance, that highly expressive face dominates the composition. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a hardness acquired on the city's alleys, his black plumed appendages demonic, a unclothed adolescent creating chaos in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a British museum, represents one of the most discomfiting artworks ever painted. Observers feel completely disoriented looking at it. The god of love, whose arrows inspire people with often painful longing, is shown as a extremely real, vividly illuminated unclothed figure, straddling toppled-over objects that comprise stringed devices, a music manuscript, metal armor and an architect's T-square. This heap of items echoes, intentionally, the geometric and construction gear strewn across the ground in the German master's engraving Melencolia I – except in this case, the melancholic mess is caused by this grinning deity and the mayhem he can release.

"Love sees not with the eyes, but with the soul, / And therefore is feathered Cupid depicted blind," wrote the Bard, just before this work was created around 1601. But Caravaggio's Cupid is not unseeing. He gazes straight at you. That face – ironic and ruddy-cheeked, looking with bold confidence as he struts unclothed – is the identical one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his multiple images of the identical distinctive-appearing kid in the Eternal City at the start of the 17th century, he was the highly acclaimed religious artist in a metropolis ignited by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been depicted numerous times before and render it so fresh, so unfiltered and visceral that the horror appeared to be happening directly before you.

However there was another aspect to Caravaggio, apparent as soon as he came in Rome in the winter that ended the sixteenth century, as a artist in his early twenties with no mentor or supporter in the city, just talent and audacity. The majority of the works with which he caught the sacred metropolis's eye were everything but holy. That may be the absolute earliest hangs in London's art museum. A youth parts his red mouth in a yell 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: viewers can see the painter's dismal chamber mirrored in the murky liquid of the glass vase.

The adolescent wears a rose-colored flower in his hair – a symbol of the sex trade in Renaissance painting. Venetian painters such as Titian and Jacopo Palma portrayed courtesans holding flowers and, in a work lost in the second world war but known through images, Caravaggio represented a famous woman courtesan, clutching a bouquet to her bosom. The message of all these botanical signifiers is obvious: sex for sale.

How are we to make of the artist's erotic depictions of youths – and of a particular boy in particular? It is a inquiry that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complicated past reality is that the artist was neither the queer hero that, for instance, the filmmaker presented on screen in his twentieth-century film about the artist, nor so completely pious that, as some art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works do make overt sexual suggestions, or including propositions. It's as if Caravaggio, then a penniless young artist, aligned with Rome's prostitutes, offering himself to survive. In the Uffizi, with this idea in consideration, observers might look to another early work, the 1596 masterwork Bacchus, in which the deity of wine stares coolly at the spectator as he starts to untie the black sash of his garment.

A few years following the wine deity, what could have driven Caravaggio to create Victorious Cupid for the art collector Vincenzo Giustiniani, when he was at last growing nearly respectable with important ecclesiastical commissions? This unholy pagan god revives the sexual challenges of his early works but in a more intense, uneasy way. Half a century afterwards, its secret seemed obvious: it was a representation of Caravaggio's companion. A British traveller saw the painting in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or servant that slept with him". The name of this boy was Francesco.

The artist had been deceased for about 40 annums when this story was documented.