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A young boy cries out while his head is forcefully gripped, a large digit digging into his face as his parent's powerful hand grasps him by the neck. That moment from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's chilling portrayal of the suffering youth from the scriptural narrative. It seems as if Abraham, instructed by God to kill his son, could snap his spinal column with a single turn. Yet the father's chosen method involves the metallic grey knife he holds in his other hand, prepared to cut Isaac's neck. A certain aspect stands out – whoever posed as the sacrifice for this breathtaking work demonstrated remarkable expressive skill. Within exists not only dread, shock and pleading in his shadowed gaze but additionally profound sorrow that a protector could betray him so utterly.

He adopted a well-known biblical story and transformed it so vibrant and visceral that its terrors seemed to happen right in view of the viewer

Viewing in front of the artwork, observers identify this as a real countenance, an accurate record of a young model, because the same youth – identifiable by his tousled hair and almost dark pupils – features in two other paintings by the master. In every case, that highly emotional visage commands the composition. In Youth With a Ram, he peers playfully from the darkness while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's alleys, his black plumed wings sinister, a unclothed adolescent running riot in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a London museum, constitutes one of the most discomfiting artworks ever painted. Viewers feel completely unsettled looking at it. Cupid, whose arrows fill people with frequently agonizing desire, is portrayed as a extremely tangible, brightly lit unclothed figure, straddling overturned items that include musical devices, a music score, metal armor and an architect's T-square. This pile of possessions echoes, deliberately, the geometric and architectural gear scattered across the floor in the German master's engraving Melancholy – except in this case, the gloomy mess is caused by this grinning Cupid and the turmoil he can unleash.

"Love sees not with the eyes, but with the mind, / And therefore is winged Love depicted sightless," wrote the Bard, just before this painting was created around the early 1600s. But the painter's Cupid is not unseeing. He gazes directly at the observer. That countenance – ironic and rosy-cheeked, staring with brazen assurance as he poses naked – is the same one that screams in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-looking kid in Rome at the dawn of the seventeenth century, he was the most acclaimed religious painter in a metropolis enflamed by Catholic renewal. The Sacrifice of Isaac demonstrates why he was sought to decorate sanctuaries: he could take a biblical story that had been depicted many times before and render it so new, so unfiltered and physical that the terror seemed to be happening directly in front of the spectator.

Yet there existed another aspect to the artist, evident as soon as he arrived in the capital in the winter that concluded 1592, as a artist in his initial 20s with no teacher or supporter in the urban center, only skill and boldness. The majority of the paintings with which he captured the holy city's eye were everything but holy. That may be the very first resides in London's art museum. A young man parts his red lips in a yell of agony: while reaching out his dirty digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's dismal room reflected in the cloudy waters of the transparent vase.

The boy sports a rose-colored flower in his coiffure – a emblem of the sex trade in Renaissance art. Venetian painters such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a painting lost in the second world war but documented through images, the master represented a famous female courtesan, holding a bouquet to her chest. The message of all these botanical indicators is obvious: sex for purchase.

How are we to interpret of the artist's sensual depictions of boys – and of one adolescent in particular? It is a question that has divided his interpreters since he achieved widespread recognition in the 1980s. The complex past truth is that the painter was not the homosexual hero that, for example, Derek Jarman presented on screen in his 1986 movie Caravaggio, nor so entirely pious that, as some artistic historians improbably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His early paintings do make explicit erotic implications, or even propositions. It's as if the painter, then a penniless youthful creator, identified with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in mind, viewers might turn to another early work, the 1596 masterwork the god of wine, in which the deity of alcohol stares calmly at the spectator as he starts to undo the dark sash of his garment.

A few annums after the wine deity, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally growing almost respectable with important ecclesiastical projects? This unholy non-Christian deity resurrects the sexual provocations of his initial works but in a more intense, unsettling way. Half a century later, its hidden meaning seemed obvious: it was a representation of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own youth or servant that laid with him". The name of this boy was Francesco.

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