Who was Caravaggio's dark-feathered deity of love? What secrets this masterwork uncovers about the rogue genius

A youthful boy cries out as his skull is forcefully gripped, a large thumb pressing into his face as his father's mighty hand grasps him by the neck. That moment from Abraham's Sacrifice appears in the Florentine museum, creating unease through Caravaggio's harrowing rendition of the tormented child from the biblical account. The painting appears as if Abraham, commanded by God to sacrifice his son, could break his neck with a single twist. However the father's chosen method involves the silvery steel knife he grips in his remaining palm, ready to slit the boy's neck. One certain aspect stands out – whomever modeled as the sacrifice for this astonishing work displayed remarkable acting ability. There exists not only fear, shock and pleading in his shadowed eyes but additionally profound sorrow that a protector could abandon him so utterly.

The artist took a familiar scriptural story and made it so fresh and visceral that its terrors seemed to happen right in front of you

Viewing in front of the painting, viewers recognize this as a real countenance, an accurate depiction of a young model, because the same youth – identifiable by his disheveled locks and almost black eyes – appears in several other works by the master. In every instance, that highly emotional face dominates the composition. In John the Baptist, he peers playfully from the shadows while holding a lamb. In Victorious Cupid, he grins with a hardness learned on the city's streets, his black feathery appendages demonic, a unclothed child creating riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British gallery, constitutes one of the most embarrassing masterpieces ever painted. Observers feel totally unsettled gazing at it. The god of love, whose darts fill people with frequently agonizing desire, is shown as a very tangible, vividly lit nude form, straddling toppled-over objects that include stringed instruments, a musical manuscript, metal armour and an architect's T-square. This heap of possessions echoes, intentionally, the geometric and construction equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – save in this case, the melancholic mess is caused by this grinning Cupid and the mayhem he can unleash.

"Affection looks not with the eyes, but with the soul, / And therefore is feathered Love depicted sightless," wrote the Bard, just before this painting was produced around the early 1600s. But the painter's Cupid is not blind. He stares directly at the observer. That countenance – sardonic and ruddy-faced, staring with brazen confidence as he struts naked – is the same one that screams in terror in Abraham's Test.

As the Italian master painted his three images of the identical distinctive-looking youth in the Eternal City at the start of the seventeenth century, he was the most celebrated religious artist in a city enflamed by Catholic renewal. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could take a scriptural story that had been depicted many occasions previously and make it so fresh, so unfiltered and visceral that the terror appeared to be occurring immediately before you.

However there was a different side to Caravaggio, evident as soon as he came in the capital in the cold season that ended 1592, as a painter in his initial 20s with no mentor or supporter in the city, only skill and audacity. Most of the works with which he caught the holy metropolis's eye were anything but holy. That may be the absolute earliest hangs in London's art museum. A youth parts his red lips in a scream of pain: while reaching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern the painter's dismal room mirrored in the cloudy liquid of the transparent vase.

The adolescent wears a rose-colored blossom in his hair – a symbol of the erotic commerce in Renaissance art. Venetian painters such as Tiziano and Palma Vecchio portrayed courtesans holding flowers and, in a work lost in the second world war but documented through images, Caravaggio portrayed a renowned female prostitute, holding a posy to her chest. The meaning of all these botanical signifiers is obvious: sex for sale.

How are we to make of Caravaggio's erotic depictions of boys – and of one boy in particular? It is a inquiry that has divided his interpreters since he gained widespread recognition in the twentieth century. The complicated past reality is that the artist was not the homosexual hero that, for example, Derek Jarman put on film in his 1986 movie about the artist, nor so entirely pious that, as certain art historians unbelievably claim, his Youth Holding Fruit is actually a likeness of Christ.

His early works do make explicit erotic suggestions, or even offers. It's as if the painter, then a penniless young creator, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this idea in consideration, observers might turn to an additional initial work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at you as he begins to undo the dark ribbon of his garment.

A few annums following Bacchus, what could have driven the artist to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally becoming nearly respectable with important church commissions? This profane non-Christian god revives the sexual provocations of his early paintings but in a more intense, uneasy way. Half a century afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A English visitor saw the painting 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 name of this boy was Francesco.

The artist had been dead for about 40 years when this account was recorded.