What exactly was Caravaggio's dark-feathered deity of love? The secrets that masterpiece reveals about the rogue genius

A youthful lad cries out while his head is forcefully held, a large digit pressing into his cheek as his father's powerful hand grasps him by the neck. That moment from The Sacrifice of Isaac visits the Florentine museum, evoking distress through Caravaggio's harrowing rendition of the suffering youth from the biblical account. It seems as if Abraham, instructed by the Divine to kill his offspring, could snap his neck with a single turn. Yet the father's preferred approach involves the metallic steel blade he grips in his other palm, ready to cut Isaac's neck. One definite aspect stands out – whomever modeled as Isaac for this astonishing work displayed remarkable acting ability. Within exists not just fear, shock and begging in his shadowed gaze but additionally profound grief that a guardian could abandon him so utterly.

He took a well-known biblical tale and transformed it so fresh and raw that its terrors appeared to happen right in front of the viewer

Standing in front of the artwork, observers recognize this as a real face, an precise record of a adolescent subject, because the identical boy – identifiable by his disheveled hair and almost dark pupils – appears in two other works by the master. In each instance, that highly emotional visage dominates the composition. In John the Baptist, he peers playfully from the shadows while embracing a ram. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his black plumed appendages sinister, a unclothed child running riot in a well-to-do residence.

Victorious Cupid, currently displayed at a British gallery, represents one of the most discomfiting artworks ever created. Observers feel totally disoriented looking at it. The god of love, whose darts inspire people with often painful desire, is shown as a very real, brightly illuminated nude form, standing over toppled-over objects that comprise musical devices, a music manuscript, plate armour and an architect's ruler. This pile of items echoes, intentionally, the geometric and architectural equipment strewn across the floor in Albrecht Dürer's engraving Melencolia I – except here, the gloomy mess is caused by this smirking deity and the mayhem he can unleash.

"Love sees not with the vision, but with the mind, / And therefore is feathered Cupid depicted blind," wrote Shakespeare, just before this work was produced around 1601. But Caravaggio's Cupid is not blind. He gazes straight at you. That face – ironic and rosy-cheeked, looking with brazen confidence as he struts unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

As the Italian master created his three images of the identical unusual-looking youth in Rome at the start of the seventeenth century, he was the most celebrated religious painter in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was sought to decorate churches: he could adopt a biblical narrative that had been portrayed many times before and make it so new, so unfiltered and physical that the horror seemed to be happening directly in front of the spectator.

Yet there was a different side to Caravaggio, apparent as quickly as he arrived in the capital in the winter that concluded the sixteenth century, as a painter in his initial twenties with no teacher or patron in the urban center, only skill and audacity. The majority of the paintings with which he caught the holy city's eye were everything but holy. That could be the absolute first resides in London's National Gallery. A young man opens his crimson mouth in a yell of agony: while stretching out his filthy fingers for a cherry, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can see Caravaggio's dismal room reflected in the cloudy liquid of the transparent container.

The adolescent sports a pink flower in his coiffure – a emblem of the sex trade in early modern art. Venetian painters such as Titian and Jacopo Palma depicted prostitutes holding blooms and, in a work destroyed in the second world war but documented through images, the master represented a renowned female courtesan, holding a posy to her chest. The meaning of all these botanical indicators is clear: intimacy for purchase.

How are we to interpret of Caravaggio's erotic portrayals of youths – and of a particular adolescent in specific? It is a question that has split his commentators since he achieved mega-fame in the 1980s. The complex historical truth is that the painter was neither the homosexual hero that, for instance, the filmmaker put on film in his 1986 film about the artist, nor so completely pious that, as some art historians improbably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His initial works indeed offer explicit sexual suggestions, or even offers. It's as if Caravaggio, then a destitute youthful artist, identified with Rome's sex workers, selling himself to live. In the Uffizi, with this idea in consideration, observers might look to another early creation, the 1596 masterpiece Bacchus, in which the deity of alcohol stares calmly at the spectator as he begins to untie the dark sash of his robe.

A few annums after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally growing almost respectable with important ecclesiastical projects? This profane non-Christian deity revives the sexual challenges of his early works but in a more intense, unsettling way. Half a century afterwards, its secret seemed clear: it was a portrait of Caravaggio's lover. A English traveller saw Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own youth or servant that slept with him". The name of this boy was Cecco.

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