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A young boy cries out while his head is firmly held, a massive digit digging into his face as his father's powerful hand grasps him by the throat. This scene from The Sacrifice of Isaac visits the Florentine museum, creating unease through the artist's harrowing portrayal of the tormented child from the scriptural account. It appears as if Abraham, commanded by the Divine to sacrifice his son, could break his spinal column with a single twist. However the father's chosen method involves the metallic grey blade he grips in his other hand, ready to cut Isaac's throat. A certain element stands out – whoever posed as the sacrifice for this breathtaking work displayed remarkable expressive skill. There exists not just dread, surprise and begging in his shadowed gaze but additionally profound grief that a guardian could betray him so completely.

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

Viewing in front of the artwork, viewers recognize this as a real countenance, an precise depiction of a adolescent model, because the same boy – recognizable by his tousled hair and almost black eyes – appears in two additional paintings by the master. In each instance, that richly expressive visage dominates the composition. In John the Baptist, he gazes playfully from the darkness while embracing a lamb. In Victorious Cupid, he smirks with a hardness learned on Rome's alleys, his black plumed appendages demonic, a naked child running chaos in a affluent residence.

Amor Vincit Omnia, currently displayed at a British museum, constitutes one of the most embarrassing artworks ever painted. Viewers feel completely unsettled gazing at it. Cupid, whose arrows fill people with often painful desire, is portrayed as a extremely tangible, brightly illuminated nude figure, straddling toppled-over objects that comprise musical devices, a musical manuscript, metal armour and an architect's ruler. This pile of possessions resembles, intentionally, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – except here, the melancholic mess is created by this grinning deity and the turmoil he can release.

"Affection sees not with the vision, but with the soul, / And therefore is feathered Love depicted sightless," wrote the Bard, just prior to this painting was produced around the early 1600s. But the painter's god is not unseeing. He gazes straight at the observer. That countenance – sardonic and ruddy-faced, looking with bold confidence as he poses naked – is the same one that screams in fear in Abraham's Test.

As the Italian master painted his multiple portrayals of the same unusual-appearing youth in the Eternal City at the start of the seventeenth century, he was the most acclaimed sacred artist in a city enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could adopt a biblical narrative that had been portrayed many occasions before and render it so new, so unfiltered and physical that the terror seemed to be occurring immediately in front of the spectator.

Yet there existed another aspect to the artist, apparent as quickly as he came in Rome in the cold season that ended the sixteenth century, as a artist in his initial 20s with no teacher or patron in the city, just talent and audacity. Most of the paintings with which he captured the holy city's eye were anything but holy. That could be the very first resides in the UK's art museum. A young man opens his red lips in a scream of agony: while reaching out his dirty digits for a fruit, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: observers can see Caravaggio's dismal chamber mirrored in the cloudy waters of the transparent container.

The adolescent sports a pink flower in his hair – a symbol of the erotic commerce in early modern art. Venetian painters such as Tiziano and Jacopo Palma depicted prostitutes grasping blooms and, in a work destroyed in the WWII but documented through images, Caravaggio represented a renowned female prostitute, clutching a bouquet to her bosom. The message of all these floral signifiers is obvious: sex for sale.

What are we to make of the artist's sensual depictions of boys – and of a particular adolescent in specific? It is a question that has split his commentators since he gained widespread recognition in the 1980s. The complex past reality is that the painter was neither the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century film Caravaggio, nor so completely pious that, as some artistic historians unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His early works indeed make overt sexual suggestions, or including offers. It's as if the painter, then a penniless youthful artist, identified with the city's prostitutes, offering himself to survive. In the Uffizi, with this idea in consideration, viewers might look to an additional initial creation, the sixteenth-century masterpiece Bacchus, in which the god of wine gazes coolly at the spectator as he begins to undo the dark ribbon of his robe.

A few annums following Bacchus, what could have motivated the artist to create Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was at last growing nearly established with prestigious church projects? This unholy non-Christian god revives the sexual provocations of his early works but in a more powerful, uneasy manner. Fifty years later, its secret seemed obvious: it was a representation of the painter's lover. 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 assistant that slept with him". The identity of this boy was Francesco.

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