What exactly was the dark-feathered god of desire? The insights this masterwork uncovers about the rebellious artist

A youthful boy screams as his skull is firmly gripped, a large digit digging into his cheek as his father's powerful palm holds him by the neck. This scene from Abraham's Sacrifice visits the Florentine museum, creating distress through the artist's harrowing portrayal of the suffering child from the biblical narrative. It seems as if the patriarch, commanded by God to kill his son, could snap his neck with a single turn. However Abraham's preferred method involves the metallic grey blade he holds in his other palm, prepared to slit the boy's neck. One certain aspect stands out – whoever modeled as the sacrifice for this astonishing piece displayed remarkable expressive skill. Within exists not only dread, shock and begging in his darkened gaze but additionally deep grief that a protector could abandon him so utterly.

He adopted a well-known biblical tale and transformed it so fresh and raw that its terrors seemed to happen directly in view of you

Standing in front of the painting, observers identify this as a actual countenance, an precise record of a adolescent subject, because the same boy – identifiable by his tousled locks and almost dark pupils – features in several additional works by the master. In each case, that highly expressive visage commands the composition. In Youth With a Ram, he gazes playfully from the darkness while holding a ram. In Victorious Cupid, he grins with a hardness acquired on the city's alleys, his dark feathery wings demonic, a unclothed adolescent running chaos in a well-to-do residence.

Victorious Cupid, currently displayed at a London gallery, constitutes one of the most embarrassing masterpieces ever created. Viewers feel completely disoriented gazing at it. The god of love, whose arrows fill people with frequently painful longing, is portrayed as a extremely tangible, vividly lit nude figure, standing over overturned items that comprise stringed devices, a musical manuscript, metal armour and an architect's T-square. This pile of possessions echoes, deliberately, the mathematical and construction equipment scattered across the floor in Albrecht Dürer's engraving Melancholy – except here, the gloomy disorder is caused by this grinning Cupid and the mayhem he can unleash.

"Affection sees not with the vision, but with the soul, / And therefore is winged Cupid painted sightless," wrote the Bard, just before this work was produced around 1601. But Caravaggio's Cupid is not unseeing. He gazes directly at you. That countenance – ironic and rosy-cheeked, staring with brazen assurance as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

When the Italian master created his multiple images of the identical unusual-looking youth in Rome at the dawn of the seventeenth century, he was the highly celebrated sacred artist in a metropolis enflamed by Catholic renewal. Abraham's Offering reveals why he was sought to adorn churches: he could take a scriptural narrative that had been depicted numerous occasions previously and render it so fresh, so unfiltered and visceral that the terror appeared to be occurring immediately before the spectator.

However there existed a different side to Caravaggio, apparent as quickly as he arrived in Rome in the cold season that concluded 1592, as a painter in his early twenties with no teacher or supporter in the city, just talent and boldness. The majority of the works with which he captured the sacred city's eye were anything but holy. That may be the very earliest hangs in the UK's National Gallery. A youth opens his crimson lips in a scream of agony: while stretching out his dirty digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: viewers can see the painter's gloomy chamber reflected in the cloudy waters of the glass vase.

The boy sports a pink blossom in his hair – a symbol of the sex trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio depicted courtesans grasping blooms and, in a painting destroyed in the WWII but documented through photographs, the master portrayed a renowned woman courtesan, clutching a bouquet to her chest. The message of all these floral signifiers is clear: sex for purchase.

How are we to make of the artist's erotic depictions of boys – and of one boy in particular? It is a question that has split his commentators ever since he achieved mega-fame in the 1980s. The complex past reality is that the painter was neither the queer hero that, for example, the filmmaker put on film in his 1986 movie Caravaggio, nor so completely devout that, as some art scholars improbably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His early paintings indeed offer overt erotic implications, or including propositions. It's as if the painter, then a destitute young artist, aligned with the city's prostitutes, offering himself to live. In the Uffizi, with this thought in mind, observers might look to another initial creation, the 1596 masterwork the god of wine, in which the deity of alcohol stares calmly at the spectator as he starts to undo the black sash of his garment.

A several annums following the wine deity, what could have driven Caravaggio to create Amor Vincit Omnia for the art collector the nobleman, when he was finally growing nearly established with prestigious church commissions? This unholy non-Christian deity resurrects the sexual provocations of his initial paintings but in a more intense, unsettling manner. Fifty years later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's companion. A English visitor viewed the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this boy was Cecco.

The painter had been dead for about forty annums when this account was recorded.