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The young boy screams as his skull is forcefully gripped, a large thumb digging into his cheek as his parent's powerful palm grasps him by the neck. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through Caravaggio's chilling rendition of the tormented youth from the scriptural narrative. The painting seems as if the patriarch, commanded by God to kill his offspring, could break his spinal column with a solitary turn. Yet the father's chosen approach involves the silvery grey blade he grips in his other palm, ready to slit the boy's neck. A certain aspect stands out – whoever posed as the sacrifice for this breathtaking work displayed extraordinary acting skill. There exists not just fear, shock and pleading in his darkened gaze but also profound grief that a guardian could abandon him so utterly.

The artist adopted a well-known scriptural tale and transformed it so vibrant and visceral that its terrors appeared to happen right in view of you

Viewing in front of the artwork, observers recognize this as a real face, an accurate record of a adolescent subject, because the identical youth – recognizable by his disheveled locks and nearly black eyes – appears in two other works by the master. In each case, that highly emotional visage dominates the composition. In John the Baptist, he peers mischievously from the shadows while holding a lamb. In Victorious Cupid, he grins with a hardness acquired on Rome's alleys, his black feathery wings demonic, a unclothed adolescent running chaos in a affluent residence.

Amor Vincit Omnia, presently displayed at a London museum, constitutes one of the most discomfiting masterpieces ever painted. Viewers feel totally unsettled looking at it. Cupid, whose darts fill people with often painful desire, is shown as a very tangible, brightly illuminated unclothed form, standing over overturned items that include stringed devices, a musical manuscript, metal armour and an builder's T-square. This pile of items resembles, deliberately, the mathematical and architectural equipment strewn across the floor in the German master's print Melencolia I – except in this case, the melancholic disorder is created by this grinning deity and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted sightless," penned Shakespeare, shortly before this painting was produced around the early 1600s. But the painter's god is not unseeing. He gazes directly at you. That countenance – ironic and ruddy-cheeked, looking with bold assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the identical unusual-looking youth in Rome at the start of the seventeenth century, he was the highly celebrated religious artist in a metropolis ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could adopt a scriptural narrative that had been portrayed many times before and make it so new, so unfiltered and physical that the terror seemed to be happening immediately before the spectator.

Yet there existed another side to the artist, evident as quickly as he came in Rome in the winter that concluded 1592, as a painter in his early 20s with no mentor or supporter in the city, only skill and audacity. The majority of the paintings with which he caught the holy metropolis's attention were anything but devout. What may be the very first hangs in the UK's National Gallery. A youth opens his crimson lips in a yell of pain: while stretching out his filthy digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern Caravaggio's gloomy room mirrored in the murky waters of the glass vase.

The boy sports a pink blossom in his coiffure – a emblem of the sex commerce in Renaissance art. Venetian artists such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a painting lost in the WWII but documented through images, the master portrayed a famous female courtesan, holding a bouquet to her bosom. The message of all these floral signifiers is obvious: sex for purchase.

What are we to make of the artist's erotic depictions of boys – and of a particular boy in specific? It is a inquiry that has divided his interpreters ever since he gained widespread recognition in the 1980s. The complicated historical reality is that the painter was neither the queer icon that, for instance, Derek Jarman put on film in his 1986 movie about the artist, nor so entirely devout that, as certain art historians unbelievably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His initial works indeed make overt sexual suggestions, or including offers. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's sex workers, selling himself to live. In the Florentine gallery, with this thought in consideration, observers might look to another initial work, the sixteenth-century masterpiece the god of wine, in which the deity of alcohol stares coolly at the spectator as he starts to untie the dark ribbon of his robe.

A several years following the wine deity, what could have driven Caravaggio to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was at last growing nearly established with important church commissions? This profane non-Christian deity resurrects the erotic challenges of his initial works but in a increasingly powerful, unsettling way. Fifty years later, its secret seemed obvious: it was a representation of the painter's companion. A English traveller saw the painting in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The name of this boy was Cecco.

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