Who exactly was Caravaggio's dark-feathered deity of love? The insights this masterpiece reveals about the rogue artist

A young lad cries out as his skull is firmly held, a large digit pressing into his cheek as his father's mighty hand grasps him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through the artist's harrowing rendition of the tormented youth from the scriptural narrative. It appears as if Abraham, commanded by the Divine to kill his offspring, could snap his neck with a solitary turn. However Abraham's preferred method involves the metallic grey blade he grips in his remaining hand, ready to slit the boy's neck. One certain aspect stands out – whoever posed as the sacrifice for this breathtaking piece demonstrated remarkable acting skill. There exists not just dread, shock and pleading in his shadowed eyes but additionally profound grief that a protector could betray him so utterly.

The artist adopted a familiar scriptural story and transformed it so fresh and visceral that its horrors seemed to happen right in view of you

Standing in front of the painting, observers identify this as a real countenance, an accurate depiction of a young subject, because the same youth – recognizable by his tousled hair and almost dark eyes – features in several other paintings by Caravaggio. In every instance, that highly emotional visage dominates the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his dark feathery wings sinister, a naked child creating riot in a affluent residence.

Victorious Cupid, presently displayed at a London gallery, constitutes one of the most discomfiting masterpieces ever painted. Observers feel totally unsettled looking at it. The god of love, whose darts fill people with often agonizing longing, is shown as a extremely real, brightly lit nude form, standing over toppled-over objects that comprise stringed devices, a music score, plate armour and an builder's ruler. This heap of possessions echoes, deliberately, the mathematical and architectural gear scattered across the floor in the German master's print Melancholy – except in this case, the melancholic mess is caused by this grinning deity and the mayhem he can release.

"Affection sees not with the eyes, but with the mind, / And thus is winged Cupid painted blind," wrote Shakespeare, just before this painting was produced around the early 1600s. But the painter's Cupid is not unseeing. He stares directly at you. That face – sardonic and ruddy-cheeked, looking with bold confidence as he struts unclothed – is the identical one that shrieks in fear in Abraham's Test.

When the Italian master painted his multiple portrayals of the same distinctive-appearing youth in Rome at the start of the seventeenth century, he was the highly acclaimed sacred painter in a city ignited by religious renewal. Abraham's Offering demonstrates why he was commissioned to adorn sanctuaries: he could adopt a biblical narrative that had been depicted many times previously and make it so fresh, so unfiltered and visceral that the horror appeared to be happening directly before the spectator.

Yet there was a different side to the artist, evident as soon as he came in the capital in the cold season that ended the sixteenth century, as a painter in his early 20s with no mentor or supporter in the city, just talent and boldness. The majority of the paintings with which he captured the sacred city's eye were everything but devout. That may be the very earliest resides in the UK's art museum. A young man parts his crimson lips in a scream of agony: while stretching out his filthy digits for a cherry, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see Caravaggio's dismal chamber mirrored in the cloudy liquid of the transparent vase.

The adolescent sports a pink flower in his hair – a emblem of the sex trade in Renaissance painting. Northern Italian artists such as Titian and Jacopo Palma portrayed courtesans grasping flowers and, in a work lost in the WWII but known through images, Caravaggio portrayed a renowned female prostitute, clutching a bouquet to her chest. The message of all these floral signifiers is clear: intimacy for purchase.

What are we to interpret of the artist's erotic depictions of youths – and of a particular boy in particular? It is a inquiry that has split his commentators ever since he achieved widespread recognition in the 1980s. The complex historical truth is that the artist was neither the queer hero that, for example, Derek Jarman presented on film in his 1986 movie about the artist, nor so entirely pious that, as certain artistic historians improbably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His early works do make explicit erotic suggestions, or even propositions. It's as if Caravaggio, then a penniless young artist, aligned with Rome's sex workers, offering himself to live. In the Florentine gallery, with this thought in consideration, observers might look to an additional initial work, the sixteenth-century masterpiece Bacchus, in which the god of wine gazes calmly at you as he starts to undo the dark sash of his garment.

A few annums following Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last becoming almost respectable with prestigious church commissions? This unholy non-Christian god resurrects the sexual challenges of his early works but in a more powerful, uneasy manner. Fifty years later, its hidden meaning seemed obvious: it was a representation of the painter's companion. A English traveller saw Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne boy or servant that laid with him". The name of this boy was Francesco.

The painter had been deceased for about forty annums when this story was documented.