Who was Caravaggio's black-winged god of love? The secrets that masterwork uncovers about the rebellious artist

The young boy screams as his skull is forcefully held, a massive digit pressing into his face as his parent's mighty hand holds him by the throat. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through the artist's chilling rendition of the suffering youth from the biblical narrative. The painting appears as if Abraham, instructed by the Divine to kill his offspring, could break his spinal column with a solitary twist. Yet the father's preferred approach involves the metallic steel knife he grips in his remaining palm, ready to cut Isaac's neck. A definite aspect remains – whomever modeled as Isaac for this breathtaking work displayed extraordinary expressive ability. There exists not only dread, shock and begging in his shadowed gaze but also profound grief that a protector could abandon him so utterly.

The artist adopted a well-known biblical tale and made it so fresh and visceral that its horrors appeared to unfold directly in view of the viewer

Viewing in front of the painting, observers recognize this as a actual face, an accurate record of a young subject, because the same youth – identifiable by his disheveled locks and almost dark pupils – features in two other paintings by Caravaggio. In each instance, that richly expressive face commands the scene. In John the Baptist, he gazes playfully from the darkness while embracing a lamb. In Amor Vincit Omnia, he grins with a toughness learned on the city's streets, his black plumed wings demonic, a unclothed child running chaos in a well-to-do residence.

Victorious Cupid, currently displayed at a London museum, represents one of the most discomfiting masterpieces ever created. Observers feel totally disoriented gazing at it. Cupid, whose darts inspire people with frequently painful desire, is shown as a very real, vividly lit unclothed figure, standing over toppled-over objects that comprise musical instruments, a music manuscript, metal armor and an builder's ruler. This heap of items echoes, intentionally, the mathematical and construction gear scattered across the floor in the German master's print Melencolia I – except in this case, the melancholic mess is created by this grinning Cupid and the turmoil he can release.

"Love looks not with the vision, but with the mind, / And thus is winged Cupid depicted blind," wrote the Bard, shortly before this painting was produced around 1601. But the painter's god is not unseeing. He gazes directly at the observer. That countenance – ironic and ruddy-cheeked, staring with brazen confidence as he struts unclothed – is the identical one that screams in terror in Abraham's Test.

As the Italian master created his multiple images of the same unusual-appearing youth in the Eternal City at the start of the seventeenth century, he was the most celebrated religious painter in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been portrayed many occasions previously and make it so new, so raw and physical that the terror seemed to be happening immediately in front of the spectator.

Yet there existed another aspect to Caravaggio, evident as quickly as he arrived in the capital in the cold season that concluded 1592, as a painter in his initial 20s with no mentor or supporter in the urban center, only skill and boldness. Most of the paintings with which he caught the sacred metropolis's attention were everything but holy. What could be the very first hangs in the UK's art museum. A young man opens his crimson mouth in a yell of agony: while stretching out his dirty digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can discern Caravaggio's gloomy chamber mirrored in the cloudy waters of the glass container.

The boy wears a pink blossom in his coiffure – a emblem of the sex commerce in Renaissance art. Venetian painters such as Tiziano and Jacopo Palma depicted courtesans grasping flowers and, in a work destroyed in the second world war but documented through photographs, Caravaggio portrayed a famous female courtesan, clutching a bouquet to her chest. The message of all these floral indicators is clear: sex for sale.

What are we to make of the artist's erotic portrayals of youths – and of one adolescent in particular? It is a question that has split his interpreters since he achieved widespread recognition in the twentieth century. The complex past truth is that the painter was not the queer hero that, for instance, Derek Jarman presented on film in his 1986 film about the artist, nor so completely devout that, as certain art scholars improbably claim, his Youth Holding Fruit is actually a likeness of Jesus.

His early paintings do offer overt erotic implications, or even propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with Rome's prostitutes, selling himself to live. In the Florentine gallery, with this thought in consideration, observers might look to an additional early work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol gazes coolly at you as he begins to untie the dark sash of his garment.

A few annums after the wine deity, what could have motivated the artist to paint Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally becoming nearly established with prestigious ecclesiastical projects? This unholy pagan god resurrects the erotic challenges of his early works but in a more intense, unsettling manner. Half a century later, its secret seemed clear: it was a portrait of the painter's companion. A British visitor viewed Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or servant that laid with him". The identity of this adolescent was Francesco.

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