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

A youthful lad screams as his skull is forcefully gripped, a massive digit pressing into his face as his father's mighty palm holds him by the throat. This moment from The Sacrifice of Isaac visits the Florentine museum, evoking unease through the artist's harrowing portrayal of the tormented child from the scriptural account. The painting seems as if the patriarch, instructed by God to sacrifice his son, could break his spinal column with a single turn. However the father's chosen approach involves the metallic grey knife he holds in his remaining hand, prepared to slit the boy's neck. One certain aspect remains – whomever modeled as the sacrifice for this breathtaking piece displayed extraordinary expressive skill. Within exists not only fear, shock and begging in his darkened gaze but also deep sorrow that a guardian could abandon him so utterly.

He took a familiar scriptural story and transformed it so vibrant and visceral that its horrors seemed to happen right in view of you

Viewing in front of the painting, viewers identify this as a real countenance, an accurate record of a young subject, because the same boy – recognizable by his disheveled locks and nearly dark pupils – appears in several additional paintings by Caravaggio. In each case, that richly expressive face commands the scene. In John the Baptist, he peers mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a hardness acquired on Rome's streets, his dark plumed appendages demonic, a unclothed adolescent running riot in a affluent dwelling.

Victorious Cupid, presently exhibited at a London gallery, constitutes one of the most discomfiting artworks ever painted. Observers feel completely unsettled looking at it. The god of love, whose darts inspire people with often agonizing desire, is portrayed as a very tangible, vividly illuminated unclothed figure, straddling toppled-over objects that comprise stringed instruments, a music score, plate armour and an builder's ruler. This heap of items resembles, deliberately, the mathematical and architectural equipment scattered across the ground in the German master's print Melencolia I – except here, the melancholic mess is caused by this grinning deity and the turmoil he can unleash.

"Love looks not with the vision, but with the mind, / And therefore is winged Cupid painted blind," penned the Bard, just before this work was created around 1601. But the painter's god is not unseeing. He stares directly at you. That countenance – sardonic and rosy-faced, staring with bold assurance as he struts unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When the Italian master created his three images of the same unusual-looking youth in the Eternal City at the start of the 17th century, he was the most acclaimed religious painter in a metropolis enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted numerous times previously and make it so new, so unfiltered and visceral that the terror seemed to be occurring directly in front of the spectator.

Yet there existed another aspect to Caravaggio, evident as soon as he came in Rome in the winter that concluded 1592, as a artist in his early 20s with no mentor or supporter in the urban center, only talent and audacity. The majority of the paintings with which he caught the holy metropolis's attention were anything but holy. That may be the absolute first hangs in London's National Gallery. A youth parts his red mouth in a yell of pain: while stretching out his dirty digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can see Caravaggio's gloomy room reflected in the murky liquid of the glass vase.

The adolescent wears a pink flower in his hair – a emblem of the sex trade in early modern painting. Northern Italian artists such as Tiziano and Jacopo Palma depicted prostitutes holding blooms and, in a painting lost in the second world war but known through photographs, the master represented a famous female prostitute, holding a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for sale.

What are we to interpret of the artist's sensual portrayals of boys – and of a particular 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 neither the queer hero that, for example, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so completely devout that, as some artistic scholars unbelievably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His initial works do offer overt sexual suggestions, or even offers. It's as if Caravaggio, then a destitute young creator, identified with the city's prostitutes, selling himself to live. In the Florentine gallery, with this thought in mind, observers might turn to another early creation, the sixteenth-century masterwork the god of wine, in which the deity of alcohol gazes calmly at the spectator as he begins to undo the black ribbon of his garment.

A several years after the wine deity, what could have motivated Caravaggio to paint Victorious Cupid for the art collector the nobleman, when he was finally becoming almost respectable with prestigious ecclesiastical projects? This unholy non-Christian god revives the erotic challenges of his early paintings but in a increasingly intense, unsettling manner. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A British visitor viewed the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The name of this boy was Francesco.

The artist had been dead for about forty annums when this story was recorded.