Who was Caravaggio's black-winged deity of desire? What secrets that masterpiece uncovers about the rebellious artist

The young boy cries out while his head is firmly gripped, a massive thumb digging into his cheek as his parent's mighty hand holds him by the throat. This scene from Abraham's Sacrifice visits the Florentine museum, creating distress through the artist's harrowing portrayal of the suffering child from the scriptural narrative. The painting seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could break his spinal column with a single twist. However the father's preferred method involves the metallic steel blade he holds in his remaining hand, ready to slit the boy's throat. A definite aspect stands out – whomever posed as Isaac for this astonishing work displayed extraordinary expressive ability. There exists not just fear, shock and pleading in his shadowed eyes but additionally profound sorrow that a protector could betray him so utterly.

He took a familiar biblical tale and transformed it so fresh and visceral that its horrors appeared to happen right in view of you

Viewing before the painting, viewers identify this as a real countenance, an accurate record of a young model, because the same boy – identifiable by his tousled locks and almost black eyes – features in two other works by Caravaggio. In every instance, that highly emotional visage commands the composition. In Youth With a Ram, he peers mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his black plumed appendages sinister, a unclothed adolescent running riot in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a British museum, constitutes one of the most discomfiting artworks ever painted. Viewers feel completely disoriented gazing at it. The god of love, whose darts inspire people with frequently painful desire, is portrayed as a extremely real, brightly illuminated nude figure, straddling overturned items that include stringed devices, a musical manuscript, metal armor and an builder's ruler. This pile of items resembles, intentionally, the mathematical and construction equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – save in this case, the gloomy mess is created by this grinning Cupid and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And thus is winged Cupid depicted blind," wrote the Bard, just before this painting was created around 1601. But the painter's god is not blind. He gazes straight at the observer. That face – sardonic and ruddy-cheeked, looking with brazen confidence as he poses naked – is the same one that shrieks in fear in Abraham's Test.

As the Italian master painted his three images of the same unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the highly celebrated religious artist in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could take a scriptural narrative that had been depicted many times before and make it so new, so raw and physical that the horror seemed to be happening directly in front of you.

However there was another aspect to Caravaggio, apparent as soon as he came in the capital in the cold season that concluded the sixteenth century, as a painter in his early twenties with no mentor or patron in the city, just talent and boldness. Most of the paintings with which he captured the sacred city's attention were everything but devout. What could be the very first hangs in the UK's art museum. A youth parts his crimson mouth in a scream of agony: while stretching out his filthy fingers for a fruit, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid squalor: observers can discern the painter's gloomy room mirrored in the murky liquid of the glass vase.

The adolescent wears a pink flower in his coiffure – a symbol of the sex commerce in Renaissance painting. Venetian painters such as Tiziano and Palma Vecchio portrayed courtesans grasping flowers and, in a painting destroyed in the second world war but known through photographs, Caravaggio represented a famous woman prostitute, clutching a posy to her chest. The message of all these floral signifiers is obvious: intimacy for purchase.

How are we to interpret of the artist's sensual portrayals of boys – and of one adolescent in particular? It is a inquiry that has split his interpreters since he gained widespread recognition in the 1980s. The complicated past truth is that the artist was neither the homosexual icon that, for instance, the filmmaker put on screen in his 1986 movie about the artist, nor so entirely pious that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His early paintings do offer overt sexual implications, or even offers. It's as if Caravaggio, then a destitute young creator, aligned with Rome's sex workers, offering himself to survive. In the Florentine gallery, with this idea in mind, viewers might turn to another initial creation, the sixteenth-century masterpiece Bacchus, in which the god of alcohol gazes calmly at you as he begins to untie the dark sash of his garment.

A several annums following Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the art collector the nobleman, when he was finally becoming almost respectable with prestigious church commissions? This unholy pagan god resurrects the sexual provocations of his early works but in a increasingly intense, uneasy manner. Fifty years afterwards, its secret seemed obvious: it was a representation of Caravaggio's companion. A English visitor saw Victorious Cupid in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] own boy or servant that laid with him". The identity of this boy was Francesco.

The painter had been deceased for about 40 annums when this story was documented.